Differential expression analysis–MAST cpm det mode
Siming Zhao
2019-03-25
Last updated: 2019-03-26
Checks: 5 1
Knit directory: cropseq/
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MAST cpm det mode from https://github.com/csoneson/conquer_comparison/blob/master/scripts/apply_MASTcpmDetRate.R.
Load functions and setup
source("code/summary_functions.R")
source("code/DE_functions.R")
library(dplyr)
library(gtools)
library(data.table)
load("data/DE_input.Rd")
displayout <- function(res){
summ_pvalues(res$pval)
print(paste0("There are ",dim(res[res$fdr < 0.1,])[1], " genes passed FDR <0.1 cutoff"))
print(knitr::kable(signif(as.matrix(head(res)),digit=2)))
}Load data for a particular locus
glocus <- "VPS45"
Nperm <- 5
gcount <- dm[1:(dim(dm)[1]-76), colnames(dm1dfagg)[dm1dfagg[glocus,] >0 & nlocus==1]]
ncount <- dm[1:(dim(dm)[1]-76), colnames(dm1dfagg)[dm1dfagg["neg",] >0 & nlocus==1]]Load data for a particular gRNA
Run MAST–No filtering
y <- DE_process(gcount, ncount, filtcpm=-1, filtpercent=0.2, perm=F)
res <- run_MASTcpmDetRate(y)Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")displayout(res)
[1] "There are 2 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------- -------- ------ ------ --------- ------
NCAPH2 5.0e-07 0.014 -0.42 0.160 -1.00
VPS45 2.8e-06 0.041 1.70 0.140 4.50
WDR73 2.1e-04 1.000 1.50 0.150 3.80
POMK 2.9e-04 1.000 NaN NaN NaN
HES6 3.0e-04 1.000 0.20 0.098 0.63
ARAF 3.4e-04 1.000 -1.50 0.140 -4.00Permutation
for (n in 1:Nperm){
y <- DE_process(gcount, ncount, filtcpm=-1, filtpercent=0.2, perm=T)
res <- run_MASTcpmDetRate(y)
displayout(res)
}Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
--------- -------- ---- ------ --------- -----
ZNF576 0.00016 1 -1.60 0.160 -4.1
FUK 0.00022 1 NaN NaN NaN
C1orf131 0.00035 1 -1.60 0.160 -4.1
PTTG1IP 0.00037 1 0.21 0.025 1.3
MT-ND6 0.00041 1 -1.50 0.170 -3.7
CSNK1D 0.00048 1 1.10 0.130 3.1Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------- -------- ---- ------ --------- -----
AMD1 4.4e-05 1 0.59 0.100 1.9
TSR2 4.4e-04 1 -1.10 0.130 -2.9
TOMM70 5.4e-04 1 -1.40 0.160 -3.4
CEP250 5.8e-04 1 1.10 0.083 3.9
DNPH1 7.6e-04 1 0.54 0.120 1.6
FXN 7.6e-04 1 -1.40 0.160 -3.5Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------------- -------- ----- ------ --------- -----
ZMYM1 8.5e-06 0.25 NaN NaN NaN
MTMR2 2.6e-05 0.39 -1.90 0.160 -4.7
RP11-113K21.5 1.1e-04 1.00 -1.70 0.160 -4.3
TMEM176B 2.0e-04 1.00 NaN NaN NaN
LRCH3 2.1e-04 1.00 -0.90 0.130 -2.5
RTN1 3.8e-04 1.00 0.77 0.046 3.6Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------------ -------- ---- ------- --------- ------
RAE1 7.8e-05 1 1.500 0.13 4.20
NSD1 2.7e-04 1 -0.078 0.17 -0.19
RP11-7O14.1 3.2e-04 1 NaN NaN NaN
UGDH 4.7e-04 1 1.600 0.16 4.00
THUMPD2 5.0e-04 1 0.057 0.16 0.14
TACC1 8.0e-04 1 0.500 0.12 1.50Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------------- -------- ---- ------ --------- -----
CTD-2547G23.4 0.00015 1 -0.87 0.053 -3.8
UBASH3B 0.00033 1 0.52 0.027 3.1
ZNF582 0.00050 1 -0.96 0.065 -3.8
ARCN1 0.00066 1 1.60 0.180 3.9
PPP1R1C 0.00070 1 NaN NaN NaN
KIF1B 0.00092 1 1.10 0.110 3.4Run MAST– filtering cpm > 0 in more than 0.03 cells
y <- DE_process(gcount, ncount, filtcpm=filtcpm, filtpercent=filtpercent, perm=F)
res <- run_MASTcpmDetRate(y)Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")displayout(res)
[1] "There are 2 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------- -------- ------- ------ --------- ------
NCAPH2 2.0e-07 0.0024 -0.43 0.170 -1.00
VPS45 4.0e-06 0.0240 1.60 0.140 4.40
WDR73 2.5e-04 0.7800 1.40 0.150 3.80
HES6 3.7e-04 0.7800 0.21 0.098 0.66
A2M 3.7e-04 0.7800 -0.69 0.180 -1.60
ARAF 3.9e-04 0.7800 -1.50 0.150 -4.00Permutation
for (n in 1:Nperm){
y <- DE_process(gcount, ncount, filtcpm=filtcpm, filtpercent=filtpercent, perm=T)
res <- run_MASTcpmDetRate(y)
displayout(res)
}Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------- -------- ----- ------ --------- -----
HS2ST1 4.7e-05 0.56 1.20 0.160 3.0
SLC31A2 1.0e-04 0.59 0.58 0.034 3.1
ATPAF1 3.2e-04 0.91 -0.73 0.150 -1.9
SPG7 4.1e-04 0.91 0.60 0.140 1.6
ZNF214 4.9e-04 0.91 0.57 0.031 3.2
ATG4D 5.1e-04 0.91 -1.00 0.150 -2.6Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
---------- -------- ---- ------ --------- ------
NUPL2 0.00014 1 1.10 0.160 2.80
EMC10 0.00046 1 -1.40 0.150 -3.70
JTB 0.00072 1 0.13 0.044 0.64
HSPBAP1 0.00075 1 0.73 0.041 3.60
UBE2Q2 0.00094 1 -0.21 0.170 -0.50
KIAA1324L 0.00100 1 0.70 0.084 2.40Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
--------- -------- ----- ------ --------- ------
C12orf73 3.8e-05 0.43 1.50 0.16 3.80
DICER1 7.3e-05 0.43 1.40 0.17 3.30
ULK3 1.5e-04 0.59 0.38 0.16 0.94
ZFPL1 2.3e-04 0.68 -1.20 0.14 -3.30
ZDHHC9 3.7e-04 0.84 -1.30 0.16 -3.20
TMBIM4 4.6e-04 0.84 0.44 0.16 1.10Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
--------- -------- ----- ------ --------- -----
MAP3K3 0.00034 0.97 0.940 0.064 3.70
LENG8 0.00034 0.97 1.400 0.120 3.90
PRELID3B 0.00067 0.97 0.940 0.180 2.20
BORCS7 0.00089 0.97 0.810 0.066 3.20
RDX 0.00100 0.97 0.085 0.026 0.53
AK6 0.00100 0.97 0.240 0.086 0.84Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------------- -------- ---- ------ --------- ------
PPP1R14C 0.00033 1 -1.5 0.180 -3.40
GALE 0.00039 1 -1.6 0.190 -3.70
RP11-351D16.3 0.00046 1 NaN NaN NaN
PDHX 0.00057 1 -0.2 0.170 -0.48
ZNF467 0.00066 1 -0.9 0.061 -3.60
TMA16 0.00071 1 1.3 0.150 3.40Run MAST– filtering cpm > 0 in more than 0.2 cells
y <- DE_process(gcount, ncount, filtcpm=filtcpm, filtpercent=filtpercent, perm=F)
res <- run_MASTcpmDetRate(y)Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")displayout(res)
[1] "There are 2 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------- -------- ------- ------ --------- ------
NCAPH2 3.0e-07 0.0022 -0.50 0.170 -1.20
VPS45 7.7e-06 0.0290 1.60 0.140 4.30
ARAF 3.2e-04 0.7000 -1.50 0.150 -4.00
WDR73 4.0e-04 0.7000 1.40 0.150 3.70
HES6 5.4e-04 0.7000 0.23 0.095 0.73
PDLIM2 5.9e-04 0.7000 -1.40 0.170 -3.40Permutation
for (n in 1:Nperm){
y <- DE_process(gcount, ncount, filtcpm=filtcpm, filtpercent=filtpercent, perm=T)
res <- run_MASTcpmDetRate(y)
displayout(res)
}Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------------- -------- ----- ------ --------- -----
CTC-338M12.3 0.00037 0.79 1.30 0.170 3.2
C1orf35 0.00052 0.79 -0.77 0.093 -2.5
TLE4 0.00060 0.79 1.20 0.180 2.8
SLC25A46 0.00060 0.79 1.40 0.140 3.9
GGCX 0.00073 0.79 1.40 0.130 3.8
PRNP 0.00079 0.79 -0.63 0.170 -1.6Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------------- -------- ----- ------ --------- -----
PRMT5 5.2e-05 0.39 0.58 0.0800 2.1
ECH1 1.5e-04 0.56 -0.75 0.1300 -2.1
RP11-706O15.1 2.3e-04 0.57 1.20 0.0980 3.9
LMNA 6.2e-04 0.84 1.10 0.1900 2.6
TRMT112 7.4e-04 0.84 0.34 0.0074 4.0
ARG2 8.9e-04 0.84 -1.30 0.1600 -3.2Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
------- -------- ----- ------- --------- ------
KDM5A 0.00012 0.88 -1.700 0.160 -4.40
RPF2 0.00045 0.96 1.300 0.130 3.60
ARID1A 0.00063 0.96 0.990 0.120 2.80
RAB2A 0.00073 0.96 -0.960 0.073 -3.60
NME3 0.00074 0.96 1.200 0.190 2.80
EWSR1 0.00076 0.96 -0.083 0.020 -0.59Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 0 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
---------- -------- ----- ------ --------- ----
TMEM41A 2.7e-05 0.20 1.70 0.130 4.6
LINC00467 9.7e-05 0.36 0.73 0.150 1.9
VAPA 2.8e-04 0.55 0.68 0.038 3.5
DDX50 2.9e-04 0.55 0.83 0.130 2.3
RAB14 7.7e-04 1.00 0.22 0.130 0.6
KIZ 8.4e-04 1.00 0.78 0.049 3.5Warning: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated")
[1] "There are 1 genes passed FDR <0.1 cutoff"
pval fdr logFC varLogFC z
-------- -------- ------ ------ --------- ------
JAM2 7.5e-06 0.057 -1.30 0.170 -3.10
POLR2H 4.0e-04 1.000 0.18 0.100 0.56
TERF2IP 8.1e-04 1.000 -0.88 0.130 -2.40
ANAPC13 1.0e-03 1.000 0.64 0.049 2.90
ZNF720 1.2e-03 1.000 -1.30 0.150 -3.40
H1FX 1.4e-03 1.000 0.76 0.091 2.50Parameters used
- We used data processed after QC step here.
- targeted locus, choose VPS45.
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] gridExtra_2.3 dplyr_0.7.8
[3] gtools_3.8.1 data.table_1.12.0
[5] MAST_1.8.2 SingleCellExperiment_1.4.0
[7] DESeq2_1.22.2 SummarizedExperiment_1.12.0
[9] DelayedArray_0.8.0 BiocParallel_1.16.0
[11] matrixStats_0.54.0 Biobase_2.42.0
[13] GenomicRanges_1.34.0 GenomeInfoDb_1.18.1
[15] IRanges_2.16.0 S4Vectors_0.20.1
[17] BiocGenerics_0.28.0 edgeR_3.24.3
[19] limma_3.38.2 lattice_0.20-38
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.2.6 bit64_0.9-7
[4] RColorBrewer_1.1-2 progress_1.2.0 rprojroot_1.3-2
[7] tools_3.5.1 backports_1.1.2 R6_2.3.0
[10] rpart_4.1-13 Hmisc_4.1-1 DBI_1.0.0
[13] lazyeval_0.2.1 colorspace_1.3-2 nnet_7.3-12
[16] tidyselect_0.2.5 prettyunits_1.0.2 bit_1.1-14
[19] compiler_3.5.1 git2r_0.23.0 htmlTable_1.12
[22] scales_1.0.0 checkmate_1.8.5 genefilter_1.64.0
[25] stringr_1.4.0 digest_0.6.18 foreign_0.8-71
[28] rmarkdown_1.10 XVector_0.22.0 base64enc_0.1-3
[31] pkgconfig_2.0.2 htmltools_0.3.6 highr_0.7
[34] htmlwidgets_1.3 rlang_0.3.1 rstudioapi_0.10
[37] RSQLite_2.1.1 bindr_0.1.1 acepack_1.4.1
[40] RCurl_1.95-4.11 magrittr_1.5 GenomeInfoDbData_1.2.0
[43] Formula_1.2-3 Matrix_1.2-15 Rcpp_1.0.0
[46] munsell_0.5.0 abind_1.4-5 stringi_1.3.1
[49] yaml_2.2.0 zlibbioc_1.28.0 plyr_1.8.4
[52] blob_1.1.1 crayon_1.3.4 splines_3.5.1
[55] annotate_1.60.0 hms_0.4.2 locfit_1.5-9.1
[58] knitr_1.20 pillar_1.3.1 geneplotter_1.60.0
[61] reshape2_1.4.3 XML_3.98-1.16 glue_1.3.0
[64] evaluate_0.12 latticeExtra_0.6-28 gtable_0.2.0
[67] purrr_0.3.2 assertthat_0.2.0 ggplot2_3.1.0
[70] xtable_1.8-3 survival_2.43-1 tibble_2.0.1
[73] AnnotationDbi_1.44.0 memoise_1.1.0 workflowr_1.2.0
[76] bindrcpp_0.2.2 cluster_2.0.7-1