Last updated: 2019-04-03
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Knit directory: cropseq/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6426414 | simingz | 2019-03-27 | MAST results |
| html | 6426414 | simingz | 2019-03-27 | MAST results |
| Rmd | f433017 | simingz | 2019-03-26 | rename enrichment |
| html | f433017 | simingz | 2019-03-26 | rename enrichment |
# SNPfile: "/project2/xinhe/simingz/CROP-seq/scRNA_seq_SNP_list.txt"
module load mysql
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e '
select
K.name2,
K.name,
S.name,
S.avHet,
S.chrom,
S.chromStart,
K.txStart,
K.txEnd
from snp150 as S
left join refGene as K on
(S.chrom=K.chrom and not(K.txEnd+1000000<S.chromStart or S.chromEnd+1000000<K.txStart))
where
S.name in ("rs7148456","rs12895055","rs7170068","rs520843","rs12716973","rs2192932","rs17200916","rs1198588","rs324017","rs4151680","rs301791","rs324015","rs9882911","rs11633075","rs2027349","rs186132169","rs9661794","rs7936858","rs3861678","rs10933","rs6071578")' > /project2/xinhe/simingz/CROP-seq/cropseq/data/SNP_1000000.txtsnpfile <- "/project2/xinhe/simingz/CROP-seq/scRNA_seq_SNP_list.txt"
gRNAsnp <- read.table(snpfile, header=F, stringsAsFactors = F)
colnames(gRNAsnp) <- c("locus_SNP", "locus")
show_cisgene <- function(cisgene){
outdfall <- NULL
outstat <- rep(0,8)
names(outstat) <- c("No.cisgene", "No.cisgene(p<0.05)","No.cisgene(logFC>0)","No.cisgene(p<0.05,logFC>0)", "No.allgene", "No.allgene(p<0.05)","No.allgene(logFC>0)","No.allgene(p<0.05,logFC>0)")
for (i in 1:dim(gRNAsnp)[1]){
locsnp <- gRNAsnp[i,"locus_SNP"]
loc <- gRNAsnp[i,"locus"]
loccisgene <- unique(cisgene[cisgene[,3]==locsnp,1])
for (pfile in list.files("data/gRNA_edgeR-QLF/", paste0(loc, "_.*_edgeR-qlf_Neg1_Empricialp.Rd"))){
load(paste0("data/gRNA_edgeR-QLF/",pfile))
gRNA <- strsplit(pfile, split = "_edgeR")[[1]][1]
outdf <- cbind(locsnp, loc, gRNA,loccisgene, resEmpiricalp[loccisgene, c(1,2,9,10)])
colnames(outdf)[c(1,2,4,7,8)] <- c("locus_SNP", "locus", "cisGene", "empiricalP", "empiricalFDR")
outstat[5] <- outstat[5] + dim(resEmpiricalp)[1]
outstat[6] <- outstat[6] + dim(resEmpiricalp[resEmpiricalp$empiricalPall < 0.05,])[1]
outstat[7] <- outstat[7] + dim(resEmpiricalp[resEmpiricalp$logFC>0 ,])[1]
outstat[8] <- outstat[8] + dim(resEmpiricalp[resEmpiricalp$empiricalPall < 0.05 & resEmpiricalp$logFC>0, ])[1]
outdfall <- rbind(outdfall, outdf)
}
}
rownames(outdfall) <- NULL
outdfall <- outdfall[complete.cases(outdfall),]
outdfall[, 5:8] <- signif(outdfall[,5:8],3)
outstat[1] <- dim(outdfall)[1]
outstat[2] <- dim(outdfall[outdfall$empiricalP < 0.05,])[1]
outstat[3] <- dim(outdfall[outdfall$logFC>0 ,])[1]
outstat[4] <- dim(outdfall[outdfall$empiricalP < 0.05 & outdfall$logFC>0, ])[1]
return(list(outdfall,outstat))
}cisgene <- read.table("data/SNP_50000.txt", stringsAsFactors = F,sep="\t", header=T)
outres<- show_cisgene(cisgene)
outdfall <- outres[[1]]
write.table( outdfall , file= "data/SNP_50000_empiricalP.txt" , row.names=F, col.names=T, sep="\t", quote = F)
DT::datatable(outdfall)outstat <- outres[[2]]
outstat No.cisgene No.cisgene(p<0.05)
54 6
No.cisgene(logFC>0) No.cisgene(p<0.05,logFC>0)
31 5
No.allgene No.allgene(p<0.05)
374119 18315
No.allgene(logFC>0) No.allgene(p<0.05,logFC>0)
191101 9945 test1 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[6]-outstat[8], outstat[8]), ncol=2))
test2 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[5]-outstat[7], outstat[7]), ncol=2))Enrichment of repressed genes (logFC>0), p value is 0.229(test1, using p <0.05 genes as background), 0.219 (test2, using all genes as background).
cisgene <- read.table("data/SNP_200000.txt", stringsAsFactors = F,sep="\t", header=T)
outres<- show_cisgene(cisgene)
outdfall <- outres[[1]]
write.table( outdfall , file= "data/SNP_200000_empiricalP.txt" , row.names=F, col.names=T, sep="\t", quote = F)
DT::datatable(outdfall)outstat <- outres[[2]]
outstat No.cisgene No.cisgene(p<0.05)
152 11
No.cisgene(logFC>0) No.cisgene(p<0.05,logFC>0)
84 9
No.allgene No.allgene(p<0.05)
374119 18315
No.allgene(logFC>0) No.allgene(p<0.05,logFC>0)
191101 9945 test1 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[6]-outstat[8], outstat[8]), ncol=2))
test2 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[5]-outstat[7], outstat[7]), ncol=2))Enrichment of repressed genes (logFC>0), p value is 0.0762(test1, using p <0.05 genes as background), 0.0661 (test2, using all genes as background).
cisgene <- read.table("data/SNP_500000.txt", stringsAsFactors = F,sep="\t", header=T)
outres<- show_cisgene(cisgene)
outdfall <- outres[[1]]
write.table( outdfall , file= "data/SNP_500000_empiricalP.txt" , row.names=F, col.names=T, sep="\t", quote = F)
DT::datatable(outdfall)outstat <- outres[[2]]
outstat No.cisgene No.cisgene(p<0.05)
307 19
No.cisgene(logFC>0) No.cisgene(p<0.05,logFC>0)
167 15
No.allgene No.allgene(p<0.05)
374119 18315
No.allgene(logFC>0) No.allgene(p<0.05,logFC>0)
191101 9945 test1 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[6]-outstat[8], outstat[8]), ncol=2))
test2 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[5]-outstat[7], outstat[7]), ncol=2))Enrichment of repressed genes (logFC>0), p value is 0.0371(test1, using p <0.05 genes as background), 0.0197 (test2, using all genes as background).
cisgene <- read.table("data/SNP_1000000.txt", stringsAsFactors = F,sep="\t", header=T)
outres<- show_cisgene(cisgene)
outdfall <- outres[[1]]
write.table( outdfall , file= "data/SNP_1000000_empiricalP.txt" , row.names=F, col.names=T, sep="\t", quote = F)
DT::datatable(outdfall)outstat <- outres[[2]]
outstat No.cisgene No.cisgene(p<0.05)
576 28
No.cisgene(logFC>0) No.cisgene(p<0.05,logFC>0)
294 17
No.allgene No.allgene(p<0.05)
374119 18315
No.allgene(logFC>0) No.allgene(p<0.05,logFC>0)
191101 9945 test1 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[6]-outstat[8], outstat[8]), ncol=2))
test2 <- fisher.test(matrix(c(outstat[2]-outstat[4], outstat[4],outstat[5]-outstat[7], outstat[7]), ncol=2))
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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 knitr_1.20 whisker_0.3-2 magrittr_1.5
[5] workflowr_1.2.0 xtable_1.8-3 R6_2.3.0 stringr_1.4.0
[9] tools_3.5.1 DT_0.5 git2r_0.23.0 htmltools_0.3.6
[13] crosstalk_1.0.0 yaml_2.2.0 rprojroot_1.3-2 digest_0.6.18
[17] shiny_1.2.0 later_0.7.5 htmlwidgets_1.3 fs_1.2.6
[21] promises_1.0.1 glue_1.3.0 evaluate_0.12 mime_0.6
[25] rmarkdown_1.10 stringi_1.3.1 compiler_3.5.1 backports_1.1.2
[29] jsonlite_1.6 httpuv_1.4.5