Contrasts

Last updated: 2019-03-04

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File	Version	Author	Date	Message
Rmd	1be7385	Yasin Kaymaz	2019-03-04	initial commit

Here, the purpose is to identify genes that are exclusively expressed in In6a and In6b cell population in contrast against the background cells.

avg_logFC : log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group.
pct.1 : The percentage of cells where the gene is detected in the first group
pct.2 : The percentage of cells where the gene is detected in the second group
p_val_adj : Adjusted p-value, based on bonferroni correction using all genes in the dataset.

Differential expression of marker genes in each of the subsets:

Pvalb-Tac1 vs GABA clusters

Pvalb-Tac1 versus GABA clusters in PFC only. Pvalb-Tac1 corresponds to In6b in Lake2018 while GABA clusters are In1a, In1b, In1c, In3, In4a, In4b, In6a, In7, In8.

group1 = ("In6b")

group2 = ("In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")

In6 vs all others in BA10

In6 versus all remaining groups in BA10.

group1 = ("In6a", "In6b")

group2 = ("Ast",  "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In7", "In8")

In6a vs all others in BA10

In6a versus all remaining groups in BA10.

group1 = ("In6a")

group2 = ("Ast",  "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6b", "In7", "In8")

In6b vs all others in BA10

In6b versus all remaining groups in BA10.

group1 = ("In6b")

group2 = ("Ast",  "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")

In6a vs all other Neurons in BA10

In6a versus all remaining Neurons in BA10.

group1 = ("In6a")

group2 = ("Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6b", "In7", "In8")

In6b vs all other Neurons in BA10

In6b versus all remaining Neurons in BA10.

group1 = ("In6b")

group2 = ("Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")

Session information

sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin17.5.0 (64-bit)
Running under: macOS  10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bindrcpp_0.2.2  Seurat_2.3.3    Matrix_1.2-14   cowplot_0.9.3  
 [5] here_0.1        forcats_0.3.0   stringr_1.4.0   dplyr_0.7.6    
 [9] purrr_0.2.5     readr_1.1.1     tidyr_0.8.1     tibble_2.0.1   
[13] tidyverse_1.2.1 DT_0.4          plotly_4.8.0    ggplot2_3.1.0  

loaded via a namespace (and not attached):
  [1] readxl_1.1.0         snow_0.4-3           backports_1.1.2     
  [4] Hmisc_4.1-1          workflowr_1.1.1      plyr_1.8.4          
  [7] igraph_1.2.1         lazyeval_0.2.1       splines_3.5.0       
 [10] crosstalk_1.0.0      digest_0.6.18        foreach_1.4.4       
 [13] htmltools_0.3.6      lars_1.2             gdata_2.18.0        
 [16] magrittr_1.5         checkmate_1.8.5      cluster_2.0.7-1     
 [19] mixtools_1.1.0       ROCR_1.0-7           modelr_0.1.2        
 [22] R.utils_2.6.0        colorspace_1.4-0     rvest_0.3.2         
 [25] haven_1.1.2          crayon_1.3.4         jsonlite_1.6        
 [28] bindr_0.1.1          survival_2.42-6      zoo_1.8-3           
 [31] iterators_1.0.10     ape_5.1              glue_1.3.0          
 [34] gtable_0.2.0         kernlab_0.9-26       prabclus_2.2-6      
 [37] DEoptimR_1.0-8       scales_1.0.0         mvtnorm_1.0-8       
 [40] Rcpp_1.0.0           metap_0.9            dtw_1.20-1          
 [43] xtable_1.8-2         viridisLite_0.3.0    htmlTable_1.12      
 [46] reticulate_1.9       foreign_0.8-70       bit_1.1-14          
 [49] proxy_0.4-22         mclust_5.4.1         SDMTools_1.1-221    
 [52] Formula_1.2-3        stats4_3.5.0         tsne_0.1-3          
 [55] htmlwidgets_1.2      httr_1.3.1           gplots_3.0.1        
 [58] RColorBrewer_1.1-2   fpc_2.1-11           acepack_1.4.1       
 [61] modeltools_0.2-22    ica_1.0-2            pkgconfig_2.0.2     
 [64] R.methodsS3_1.7.1    flexmix_2.3-14       nnet_7.3-12         
 [67] later_0.7.3          tidyselect_0.2.4     rlang_0.3.1         
 [70] reshape2_1.4.3       munsell_0.5.0        cellranger_1.1.0    
 [73] tools_3.5.0          cli_1.0.1            broom_0.5.0         
 [76] ggridges_0.5.0       evaluate_0.10.1      yaml_2.2.0          
 [79] knitr_1.20           bit64_0.9-7          fitdistrplus_1.0-9  
 [82] robustbase_0.93-1    caTools_1.17.1       RANN_2.6            
 [85] pbapply_1.4-0        nlme_3.1-137         mime_0.5            
 [88] whisker_0.3-2        R.oo_1.22.0          xml2_1.2.0          
 [91] hdf5r_1.0.1          compiler_3.5.0       rstudioapi_0.8      
 [94] png_0.1-7            stringi_1.2.4        lattice_0.20-35     
 [97] trimcluster_0.1-2    diffusionMap_1.1-0   pillar_1.3.1        
[100] lmtest_0.9-36        data.table_1.11.4    bitops_1.0-6        
[103] irlba_2.3.2          httpuv_1.4.4.2       R6_2.3.0            
[106] latticeExtra_0.6-28  promises_1.0.1       KernSmooth_2.23-15  
[109] gridExtra_2.3        codetools_0.2-15     MASS_7.3-50         
[112] gtools_3.8.1         assertthat_0.2.0     rprojroot_1.3-2     
[115] withr_2.1.2          diptest_0.75-7       parallel_3.5.0      
[118] doSNOW_1.0.16        hms_0.4.2            grid_3.5.0          
[121] rpart_4.1-13         class_7.3-14         rmarkdown_1.10      
[124] segmented_0.5-3.0    Rtsne_0.15           git2r_0.23.0        
[127] shiny_1.1.0          scatterplot3d_0.3-41 lubridate_1.7.4     
[130] base64enc_0.1-3

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