Last updated: 2023-02-24
Checks: 6 1
Knit directory: duplex_sequencing_screen/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown is untracked by Git. To know which version of the R
Markdown file created these results, you’ll want to first commit it to
the Git repo. If you’re still working on the analysis, you can ignore
this warning. When you’re finished, you can run
wflow_publish
to commit the R Markdown file and build the
HTML.
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was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
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The results in this page were generated with repository version 7ac4a41. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish
or
wflow_git_commit
). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
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Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy14-[BamLeftAlign_on_data_13_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy18-[BamLeftAlign_on_data_17_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy18-[BamLeftAlign_on_data_17_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy22-[BamLeftAlign_on_data_21_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy22-[BamLeftAlign_on_data_21_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy57-[BamLeftAlign_on_data_56_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy57-[BamLeftAlign_on_data_56_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy61-[BamLeftAlign_on_data_60_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy61-[BamLeftAlign_on_data_60_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy65-[BamLeftAlign_on_data_64_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy65-[BamLeftAlign_on_data_64_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy69-[BamLeftAlign_on_data_68_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy69-[BamLeftAlign_on_data_68_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy73-[BamLeftAlign_on_data_72_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy73-[BamLeftAlign_on_data_72_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy77-[BamLeftAlign_on_data_76_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP4/Galaxy77-[BamLeftAlign_on_data_76_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy26-[BamLeftAlign_on_data_25_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy30-[BamLeftAlign_on_data_29_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy34-[BamLeftAlign_on_data_33_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy38-[BamLeftAlign_on_data_37_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy38-[BamLeftAlign_on_data_37_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy42-[BamLeftAlign_on_data_41_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy42-[BamLeftAlign_on_data_41_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy46-[BamLeftAlign_on_data_45_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy50-[BamLeftAlign_on_data_49_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy54-[BamLeftAlign_on_data_53_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy58-[BamLeftAlign_on_data_57_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy62-[BamLeftAlign_on_data_61_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy66-[BamLeftAlign_on_data_65_(alignments)].bam
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bai
Deleted: data/Consensus_Data/Novogene_lane5/GalaxyData/RP5/Galaxy70-[BamLeftAlign_on_data_69_(alignments)].bam
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_Duplex_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_Duplex_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_SSCS_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D2_SSCS_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_Duplex_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_Duplex_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_SSCS_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Low_D4_SSCS_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_Duplex_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_Duplex_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_SSCS_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D2_SSCS_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_Duplex_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_Duplex_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_SSCS_routput.csv
Deleted: data/Consensus_Data/Ranomics_Pooled/ToDo/RP4_Medium_D4_SSCS_routput_processedSep-23-2021.csv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/EnsEMBL__REST_practice.html
Deleted: data/Consensus_Data/archive/AlignmentsPractice/RP5_102121.bai
Deleted: data/Consensus_Data/archive/AlignmentsPractice/RP5_102121.bam
Deleted: data/Consensus_Data/archive/AlignmentsPractice/abl1_sequence.txt
Deleted: data/Consensus_Data/archive/AlignmentsPractice/calls_il3indep1_dcs_filtered.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/chr9130835254-130887675.dnas
Deleted: data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.bam.gz
Deleted: data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.bam.gz.bai
Deleted: data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.sam.gz
Deleted: data/Consensus_Data/archive/AlignmentsPractice/chr9_smallregion.sam.gz.bai
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_alignment.bai
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_alignment.bam
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_all_filtered.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered_calls.csv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_dcs_filtered_calls.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_alignment.bai
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_alignment.bam
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_all_filtered.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_filtered.tsv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/il3indep1_sscs_filtered_calls.csv
Deleted: data/Consensus_Data/archive/AlignmentsPractice/mnv_caller_practice.Rmd
Deleted: data/Consensus_Data/archive/AlignmentsPractice/ranomics_december_library.csv
Deleted: data/Consensus_Data/archive/abl1_cds_kinasedomain.txt
Deleted: data/Consensus_Data/archive/abl1_genomic_coordinates.csv
Deleted: data/Consensus_Data/archive/abl1_genomic_coordinates.xlsx
Deleted: data/Consensus_Data/archive/abl1_kinasedomain_coordinates.csv
Deleted: data/Consensus_Data/archive/abl1_kinasedomain_coordinates.xlsx
Deleted: data/Consensus_Data/archive/abl_exon_positions.csv
Deleted: data/Consensus_Data/archive/lane11_translation.Rmd
Deleted: data/Consensus_Data/archive/mnv_caller_cds_aligner.Rmd
Deleted: data/Consensus_Data/archive/nm_005157.6_cds.txt
Modified: data/Consensus_Data/novogene_lane15/.DS_Store
Modified: data/Consensus_Data/novogene_lane15/sample_1/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_1/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_1/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_1/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_1/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_2/.DS_Store
Modified: data/Consensus_Data/novogene_lane15/sample_2/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_2/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_2/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_2/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_3/.DS_Store
Modified: data/Consensus_Data/novogene_lane15/sample_3/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_3/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_3/duplex/variant_caller_outputs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_3/ngs/sample3a(firsthalf)/Sample3_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_3/ngs/variants_ann.csv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_3/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_3/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_4/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_5/.DS_Store
Modified: data/Consensus_Data/novogene_lane15/sample_5/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_5/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_5/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_5/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_6/.DS_Store
Modified: data/Consensus_Data/novogene_lane15/sample_6/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_6/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_6/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_6/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane15/sample_6/sscs/variant_caller_outputs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane15/sample_7/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane15/sample_7/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16a/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16a/Sample10/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample11/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample12/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample13/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample14/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16a/Sample1_combined/.DS_Store
Modified: data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16a/Sample1_combined/sscs/.DS_Store
Modified: data/Consensus_Data/novogene_lane16a/Sample2/.DS_Store
Modified: data/Consensus_Data/novogene_lane16a/Sample2/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16a/Sample2/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16a/Sample2/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16a/Sample3/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample4/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample5/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16a/Sample6/.DS_Store
Modified: data/Consensus_Data/novogene_lane16a/Sample6/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16a/Sample6/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample7/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample8/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16a/Sample9/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/.DS_Store
Modified: data/Consensus_Data/novogene_lane16b/Sample10/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample10/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample10/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample11/.DS_Store
Modified: data/Consensus_Data/novogene_lane16b/Sample15/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample15/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample15/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample15/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample2/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample2/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample3/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample3/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample4/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample4/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample5/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample5/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample6/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample6/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample6/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample6/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample7_combined/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane16b/Sample7_combined/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample8_combined/.DS_Store
Modified: data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/duplex_sorted_filtered.tsv.gz
New: data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/variant_caller_outputs/variants_ann.csv
New: data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/variant_caller_outputs/variants_unique_ann.csv
Modified: data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/variants_unique_ann.csv
New: data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/variants_unique_ann2.csv
Modified: data/Consensus_Data/novogene_lane16b/Sample9/.DS_Store
Modified: data/Consensus_Data/novogene_lane16b/Sample9/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample9/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane16b/Sample9/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane16b/Sample9/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane17/.DS_Store
New: data/Consensus_Data/novogene_lane17/duplex_2.fa
Deleted: data/Consensus_Data/novogene_lane17/sample10/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane17/sample10/sscs/sscs_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane17/sample11/duplex/duplex_sorted_filtered.tsv.gz
Deleted: data/Consensus_Data/novogene_lane17/sample11/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/.DS_Store
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/duplex/.DS_Store
Deleted: data/Consensus_Data/novogene_lane17/sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/duplex/variant_caller_outputs/variants_ann.csv
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/duplex/variant_caller_outputs/variants_unique_ann.csv
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/.DS_Store
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/.DS_Store
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/variant_caller_outputs/variants_ann.csv
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/variant_caller_outputs/variants_unique_ann.csv
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/.DS_Store
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/variant_caller_outputs/variants_ann.csv
New: data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/variant_caller_outputs/variants_unique_ann.csv
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/sscs/.DS_Store
Deleted: data/Consensus_Data/novogene_lane17/sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/sscs/variant_caller_outputs/variants_ann.csv
Modified: data/Consensus_Data/novogene_lane17/sample1_combined/sscs/variant_caller_outputs/variants_unique_ann.csv
Modified: data/Consensus_Data/novogene_lane17/sample2/.DS_Store
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New: data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/sscs/variant_caller_outputs/variants_ann.csv
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New: data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/sscs/variant_caller_outputs/variants_ann.csv
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New: data/Consensus_Data/novogene_lane17b/Sample1/duplex/variant_caller_outputs/variants_ann.csv
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Deleted: data/Consensus_Data/sscs_dcs_comparisons/sp2d2300_dcs_analysis.Rmd
Modified: data/IC50s_refseqBCRABL/Asciminib_heatmap.csv
Modified: data/IC50s_refseqBCRABL/Imatinib_heatmap.csv
Modified: data/Refs/.DS_Store
Modified: data/Refs/EGFR/.DS_Store
New: data/TP53data/41588_2018_204_MOESM5_ESM.csv
New: data/TP53data/41588_2018_204_MOESM5_ESM.xlsx
New: data/TP53data/readme.txt
New: data/TP53data/tp53_treated.pdf
New: data/TP53data/tp53_untreated.pdf
Modified: ltk_analyses.Rmd
Modified: output/.DS_Store
Modified: shinyapp/.DS_Store
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
There are no past versions. Publish this analysis with
wflow_publish()
to start tracking its development.
For the density plots:
library(viridisLite)
library("MASS")
Warning: package 'MASS' was built under R version 4.0.5
Attaching package: 'MASS'
The following object is masked from 'package:plotly':
select
The following object is masked from 'package:dplyr':
select
theme_set(theme_bw(base_size = 16))
# Get density of points in 2 dimensions.
# @param x A numeric vector.
# @param y A numeric vector.
# @param n Create a square n by n grid to compute density.
# @return The density within each square.
get_density <- function(x, y, ...) {
dens <- MASS::kde2d(x, y, ...)
ix <- findInterval(x, dens$x)
iy <- findInterval(y, dens$y)
ii <- cbind(ix, iy)
return(dens$z[ii])
}
set.seed(1)
dat <- data.frame(
x = c(
rnorm(1e4, mean = 0, sd = 0.1),
rnorm(1e3, mean = 0, sd = 0.1)
),
y = c(
rnorm(1e4, mean = 0, sd = 0.1),
rnorm(1e3, mean = 0.1, sd = 0.2)
)
)
This piece of code picks up some of the analysis done in ABL_unevenness_analysis.Rmd
Seeing how well our imatinib resistance mutants work with cosmic mutants
# source("code")
source("code/res_residues_adder.R")
source("code/variants_parser.R")
source("code/compare_samples.R")
source("code/resmuts_adder.R")
source("code/cosmic_data_adder.R")
data=read.csv("output/ABLEnrichmentScreens/Imatinib_Enrichment_2.20.23_v2.csv",header = T,stringsAsFactors = F)
data=read.csv("output/ABLEnrichmentScreens/Imat_Enrichment_bgmerged_2.22.23.csv",header = T,stringsAsFactors = F)
# class(data)
data=res_residues_adder(data)
data=cosmic_data_adder(data)
# data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs.x,netgr_obs.y))
data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs_screen1,netgr_obs_screen2))
data$resmut_cosmic="neither"
data[data$cosmic_present%in%TRUE,"resmut_cosmic"]="cosmic"
data[data$resmuts%in%TRUE,"resmut_cosmic"]="resmut"
data$resmut_cosmic=factor(data$resmut_cosmic,levels=c("neither","cosmic","resmut"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
plotly=ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Cosmic\n Observed \n Mutant"))+scale_fill_manual(values=c("gray","orange","red"))
ggplotly(plotly)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=score_screen1,y=score_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Score D0 D2")+
scale_y_continuous(name="Score D0 D4")+
labs(fill="Cosmic\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean))+geom_boxplot(aes(fill=resmut_cosmic))+scale_fill_manual(values=c("gray90","orange","red"))
# a=data%>%filter(score_mean%in%c(NA,NaN))
# a=data_cosmic%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0,cosmic_present%in%T)
Netgr Plots for putting in presentation
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+
scale_y_continuous(name="Enrichcment Score")+
scale_x_discrete(name="Mutant")+
scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
theme(axis.text.x=element_text(angle=90, hjust=1),
axis.text=element_text(size=6),
panel.grid.major = element_blank(),
panel.grid.major.y = element_blank(),
panel.background = element_blank())+
theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
theme(legend.position = "none")
a=data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494)
# ggsave("ImatinibEnrichment_Plot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean,fill=resmut_cosmic))+
geom_violin(color="black")+
geom_boxplot(color="black",width=.1)+
# geom_boxplot(color="black")+
scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))
# ggsave("ImatinibEnrichment_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-netgr_mean),y=netgr_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4")+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
theme(legend.position = "none")
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=score_screen1,y=score_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
theme(legend.position = "none")
Score plots for putting in presentation
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+
scale_y_continuous(name="Enrichcment Score")+
scale_x_discrete(name="Mutant")+
scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
theme(axis.text.x=element_text(angle=90, hjust=1),
axis.text=element_text(size=6),
panel.grid.major = element_blank(),
panel.grid.major.y = element_blank(),
panel.background = element_blank())+
theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4",sec.axis = sec_axis( trans=~., name="Doubling Time (Hours)"))+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
theme(legend.position = "none")
a=data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494)
# ggsave("ImatinibEnrichment_Plot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean,fill=resmut_cosmic))+
geom_violin(color="black")+
geom_boxplot(color="black",width=.1)+
# geom_boxplot(color="black")+
scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))
# ggsave("ImatinibEnrichment_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
# a=data%>%filter(protein_start>=242,protein_start<=494)
# a=data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1)
# b=a[order(a$score_mean,decreasing=TRUE),]
# b=b[c(1:200),]
# c=a%>%filter(!resmut_cosmic%in%"neither")
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] MASS_7.3-55 viridisLite_0.3.0 RColorBrewer_1.1-2 doParallel_1.0.15
[5] iterators_1.0.12 foreach_1.5.0 tictoc_1.0 plotly_4.9.2.1
[9] ggplot2_3.3.3 dplyr_1.0.6 stringr_1.4.0
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.31 bslib_0.3.1 purrr_0.3.4
[5] colorspace_1.4-1 vctrs_0.3.8 generics_0.0.2 htmltools_0.5.2
[9] yaml_2.2.1 utf8_1.1.4 rlang_0.4.11 jquerylib_0.1.4
[13] later_1.0.0 pillar_1.6.1 glue_1.4.1 withr_2.4.2
[17] DBI_1.1.0 lifecycle_1.0.0 munsell_0.5.0 gtable_0.3.0
[21] workflowr_1.6.2 htmlwidgets_1.5.1 codetools_0.2-16 evaluate_0.14
[25] labeling_0.3 knitr_1.28 fastmap_1.1.0 crosstalk_1.1.0.1
[29] httpuv_1.5.2 fansi_0.4.1 Rcpp_1.0.4.6 promises_1.1.0
[33] backports_1.1.7 scales_1.1.1 jsonlite_1.7.2 farver_2.0.3
[37] fs_1.4.1 digest_0.6.25 stringi_1.7.5 rprojroot_1.3-2
[41] grid_4.0.0 tools_4.0.0 magrittr_2.0.1 sass_0.4.1
[45] lazyeval_0.2.2 tibble_3.1.2 crayon_1.4.1 tidyr_1.1.3
[49] pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.12.8 assertthat_0.2.1
[53] rmarkdown_2.14 httr_1.4.2 R6_2.4.1 git2r_0.27.1
[57] compiler_4.0.0