.Rhistory

)
pdf("commonDE_chrVII.pdf")
grid.draw(venn.plotChrVII)
############################################################################
# want to know what genes are DE in all samples
getDEgenes <- function(sample) {
# first need to subset the data frame of gene expression for each aneuploid sample to include those genes that have a p-value above 0.1
allSampleDE <- subset(sample, padj<0.1)
# then subset the data frame of genes with a p-value above 0.1 to only include genes that are located on the aneuploid chromosome
#
# add column with chromosome numbers matching the GENEIDs
# find matches of GENEID in sample file to GENEID in list of genes included in analysis
matched <- intersect(sampleDE$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep
keep <- genesNoAneu$GENEID %in% matched
# subset list of genes in analysis to include only the ones matching those found in          sample file
s <- genesNoAneu[keep,]
# use c(olumn)bind to stick the chromosome #s to the sample analysis file
test <- cbind(s$GENEID, s$TXCHROM, sampleDE)
# subset to exclude first column (duplicate)
samp <- test[,2:10]
# add a column name to the chromosome column
colnames(samp)[1] <- "chr"
return(deAll)
}
############################################################################
# want to know how many genes are DE on the aneuploid chromosome in multiple aneuploid samples sharing the same aneuploid
#
# chr I
# lines 7,11,and 18
# deChrI <-
#######################################################################################
# want to know WHAT genes are DE on the aneuploid chromosome in aneuploid samples
#
sample = res4Dat
#chrom = "chrV"
getDEgenesAll <- function(sample) {
# first need to subset the data frame of gene expression for each aneuploid sample to include those genes that have a p-value above 0.1
sampleDE <- subset(sample, padj<0.1)
# then subset the data frame of genes with a p-value above 0.1 to only include genes that are located on the aneuploid chromosome
#
# add column with chromosome numbers matching the GENEIDs
# find matches of GENEID in sample file to GENEID in list of genes included in analysis
matched <- intersect(sampleDE$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep
keep <- genesNoAneu$GENEID %in% matched
# subset list of genes in analysis to include only the ones matching those found in          sample file
s <- genesNoAneu[keep,]
# use c(olumn)bind to stick the chromosome #s to the sample analysis file
test <- cbind(s$GENEID, s$TXCHROM, sampleDE)
# subset to exclude first column (duplicate)
samp <- test[,2:10]
# add a column name to the chromosome column
colnames(samp)[1] <- "chr"
# take out all chromosomes except the aneuploid one(s)
# chrom is designated when you call the function
DEAll  <- samp
return(DEAll)
}
# test it out on one of the ones I did already
# try S4
DES4all <- getDEgenesAll(res4Dat)
########################################################################################
# what DE genes are shared between samples aneuploid with the same chromosome?
# use data frames containing only DE genes in the given samples
# sample1 = genes4DE
# sample2 = genes49DE
getCommonDEgenes <- function(sample1, sample2) {
# join them together by GENEID column
chr.all <- inner_join(sample1, sample2, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matched <- intersect(chr.all$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepAll <- chr.all$GENEID %in% matched
# only keep those genes in the data frame
chr.all <- chr.all[keepAll,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenAll <- genesNoAneu$GENEID %in% matched
# put those genes in a vector
GenAll <- genesNoAneu[keepGenAll,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chr.all <- cbind(GenAll$TXCHROM, chr.all)
return(chr.all)
}
chrVAll <- getCommonDEgenes(genes4DE, genes49DE)
########################################################################################
# what DE genes are shared between samples aneuploid with the same chromosome?
# use data frames containing only DE genes in the given samples
# sample1 = genes4DE
# sample2 = genes49DE
library(dplyr)
getCommonDEgenes <- function(sample1, sample2) {
# join them together by GENEID column
chr.all <- inner_join(sample1, sample2, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matched <- intersect(chr.all$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepAll <- chr.all$GENEID %in% matched
# only keep those genes in the data frame
chr.all <- chr.all[keepAll,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenAll <- genesNoAneu$GENEID %in% matched
# put those genes in a vector
GenAll <- genesNoAneu[keepGenAll,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chr.all <- cbind(GenAll$TXCHROM, chr.all)
return(chr.all)
}
chrVAll <- getCommonDEgenes(genes4DE, genes49DE)
write.csv(chrVAll, file="chrVallDE_GC.csv")
chrVIIAll <- getCommonDEgenes(genes59DE, genes61DE)
write.csv(chrVIIAll, file="chrVIIallDE_GC.csv")
chrXIIAll <- getCommonDEgenes(genes18DE, genes77DE)
write.csv(chrXIIAll, file="chrXIIallDE_GC.csv")
## only trisomic samples
# join them together by GENEID column
chrI.tri <- inner_join(genes7DE,genes18DE, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matchedI <- intersect(chrI.tri$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepI <- chrI.tri$GENEID %in% matchedI
# only keep those genes in the data frame
chrI.tri <- chrI.tri[keepI,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGen <- genesNoAneu$GENEID %in% matchedI
# put those genes in a vector
Gen <- genesNoAneu[keepGen,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chrI.tri <- cbind(Gen$TXCHROM, chrI.tri)
# save as .csv file
write.csv(chrI.tri, file="chrITriDE.csv")
#for chromosome I, which has 3 lines that are commonly aneuploid for it, so the function won't work properly
#chrom I, all aneuploids (both trisomics plus the monosomic)
chrI.all <- inner_join(chrI.tri, genes11DE, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matchedIall <- intersect(chrI.all$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepIall <- chrI.all$GENEID %in% matchedI
# only keep those genes in the data frame
chrI.all <- chrI.all[keepIall,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenAll <- genesNoAneu$GENEID %in% matchedIall
# put those genes in a vector
GenAll <- genesNoAneu[keepGenAll,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chrI.all <- cbind(GenAll$TXCHROM, chrI.all)
# save as .csv file
write.csv(chrI.all, file="chrIAllDE.csv")
########################################################################################
# what NON-DE genes are shared between samples aneuploid with the same chromosome?
# use data frames containing only NON-DE genes in the given samples
sample1 = nonDES4c5
sample2 = nonDES49c5
getCommonNonDEgenes <- function(sample1, sample2) {
# join them together by GENEID column
chr.all <- inner_join(sample1, sample2, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matched <- intersect(chr.all$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepAll <- chr.all$GENEID %in% matched
# only keep those genes in the data frame
chr.all <- chr.all[keepAll,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenAll <- genesNoAneu$GENEID %in% matched
# put those genes in a vector
GenAll <- genesNoAneu[keepGenAll,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chr.all <- cbind(GenAll$TXCHROM, chr.all)
return(chr.all)
}
chrVNon <- getCommonNonDEgenes(nonDES4c5, nonDES49c5)
write.csv(chrVNon, file="chrVallDNonE_GC.csv")
chrVIINon <- getCommonNonDEgenes(nonDES59c7, nonDES61c7)
write.csv(chrVIINon, file="chrVIIallNonDE_GC.csv")
chrXIINon <- getCommonNonDEgenes(nonDES18c12, nonDES77c12)
write.csv(chrXIINon, file="chrXIIallNonDE_GC.csv")
## only trisomic samples
# join them together by GENEID column
chrItriNon <- inner_join(nonDES7c1,nonDES18c1, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matchedINon <- intersect(chrItriNon$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepINon <- chrItriNon$GENEID %in% matchedINon
# only keep those genes in the data frame
chrItriNon <- chrItriNon[keepINon,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenNon <- genesNoAneu$GENEID %in% matchedINon
# put those genes in a vector
GenNon <- genesNoAneu[keepGenNon,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chrItriNon <- cbind(GenNon$TXCHROM, chrItriNon)
# save as .csv file
write.csv(chrItriNon, file="chrITriNonDE.csv")
#for chromosome I, which has 3 lines that are commonly aneuploid for it, so the function won't work properly
# chrom I, all aneuploids (both trisomics plus the monosomic)
chrI.Non <- inner_join(chrItriNon, nonDES11c1, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matchedIallNon <- intersect(chrI.Non$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepIallNon <- chrI.Non$GENEID %in% matchedIallNon
# only keep those genes in the data frame
chrI.Non <- chrI.Non[keepIallNon,]
# put those genes in a vector
GenAllNon <- genesNoAneu[keepGenAllNon,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chrI.Non <- cbind(GenAllNon$TXCHROM, chrI.Non)
# save as .csv file
write.csv(chrI.Non, file="chrIAllNonDE.csv")
chrI.Non <- inner_join(chrItriNon, nonDES11c1, by="GENEID")
# match the genes to the genes in genes table that includes chromosome number
matchedIallNon <- intersect(chrI.Non$GENEID, genesNoAneu$GENEID)
# tell R which genes to keep from the chrI.tri dataframe
keepIallNon <- chrI.Non$GENEID %in% matchedIallNon
# only keep those genes in the data frame
chrI.Non <- chrI.Non[keepIallNon,]
# tell R which genes to keep from the genesNoAneu dataframe
keepGenAllNon <- genesNoAneu$GENEID %in% matchedIallNon
# put those genes in a vector
GenAllNon <- genesNoAneu[keepGenAllNon,]
# tell R to bind Gen chromosome column to chrI.tri data so we know what chromosome the genes are on
chrI.Non <- cbind(GenAllNon$TXCHROM, chrI.Non)
# save as .csv file
write.csv(chrI.Non, file="chrIAllNonDE.csv")
A <- sample(1:1000, 400, replace = FALSE);
B <- sample(1:1000, 600, replace = FALSE);
C <- sample(1:1000, 350, replace = FALSE);
D <- sample(1:1000, 550, replace = FALSE);
E <- sample(1:1000, 375, replace = FALSE);
venn.plot <- venn.diagram(
x = list(
A = genes1DE$GENEID,
B = genes2DE$GENEID,
C = genes3DE$GENEID,
D = genes5DE$GENEID,
E = genes9DE$GENEID
),
filename = NULL, #"euploid_commonDE.tiff"
col = "black",
fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
alpha = 0.50,
cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8,
1, 0.8, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
cat.cex = 1.5,
cat.fontface = "bold",
margin = 0.05
)
pdf("euploid_commonDE.pdf")
grid.draw(venn.plot)
eupLines <- list(genes1DE, genes2DE, genes3DE, genes5DE, genes9DE)
# want to get list of common DE genes in all the euploid lines
commonDEeup <- Reduce(intersect, Map("[[", eupLines, "GENEID"))
#Reduc
commonDEeup <- as.vector(commonDEeup)
write.csv(commonDEeup, file="commonDEeup.csv")
# what genes are commonly DE in aneuploid lines, but NOT located on the aneuploid chromosomes?
# genes11DE,
aneuLines <- 	list(deGenesNotAneuS4, deGenesNotAneuS7, deGenesNotAneuS8,deGenesNotAneuS59,deGenesNotAneuS77)
# want to get list of common DE genes in all the euploid lines
commonDEaneu <- Reduce(intersect, Map("[[", aneuLines, "GENEID"))
commonDEeup <- as.vector(commonDEeup)
write.csv(commonDEeup, file="commonDEeup.csv")
aneuLines4 <- 	list(deGenesNotAneuS4, deGenesNotAneuS7, deGenesNotAneuS8,deGenesNotAneuS59)
# want to get list of common DE genes in all the euploid lines
commonDEaneu4 <- Reduce(intersect, Map("[[", aneuLines4, "GENEID"))
aneuLines3 <- 	list(deGenesNotAneuS4, deGenesNotAneuS7, deGenesNotAneuS8)
# want to get list of common DE genes in all the euploid lines
commonDEaneu3 <- Reduce(intersect, Map("[[", aneuLines3, "GENEID"))
# setDT(res4Dat, keep.rownames = TRUE)[]
# setnames(res4Dat, 1, "GENEID")
# genes4DE <- subset(res4Dat,padj<0.1)
# setDT(res7Dat, keep.rownames = TRUE)[]
# setnames(res7Dat, 1, "GENEID")
# genes7DE <- subset(res7Dat,padj<0.1)
# setDT(res8Dat, keep.rownames = TRUE)[]
# setnames(res8Dat, 1, "GENEID")
# genes8DE <- subset(res8Dat,padj<0.1)
# setDT(res11Dat, keep.rownames = TRUE)[]
# setnames(res11Dat, 1, "GENEID")
# genes11DE <- subset(res11Dat,padj<0.1)
# setDT(res18Dat, keep.rownames = TRUE)[]
# setnames(res18Dat, 1, "GENEID")
# genes18DE <- subset(res18Dat,padj<0.1)
# setDT(res49Dat, keep.rownames = TRUE)[]
# setnames(res49Dat, 1, "GENEID")
# genes49DE <- subset(res49Dat,padj<0.1)
# setDT(res59Dat, keep.rownames = TRUE)[]
# setnames(res59Dat, 1, "GENEID")
# genes59DE <- subset(res59Dat,padj<0.1)
# setDT(res61Dat, keep.rownames = TRUE)[]
# setnames(res61Dat, 1, "GENEID")
# genes61DE <- subset(res61Dat,padj<0.1)
# setDT(res76Dat, keep.rownames = TRUE)[]
# setnames(res76Dat, 1, "GENEID")
# genes76DE <- subset(res76Dat,padj<0.1)
# setDT(res77Dat, keep.rownames = TRUE)[]
# setnames(res77Dat, 1, "GENEID")
# genes77DE <- subset(res77Dat,padj<0.1)
#remove genes that are commonly DE in euploid lines
# genes4DE.r <- anti_join(genes4DE, common1235.9,by="GENEID")
# genes7DE.r <- anti_join(genes7DE, common1235.9,by="GENEID")
# genes8DE.r <- anti_join(genes8DE, common1235.9,by="GENEID")
# genes11DE.r <- anti_join(genes11DE, common1235.9,by="GENEID")
# genes18DE.r <- anti_join(genes18DE, common1235.9,by="GENEID")
# genes49DE.r <- anti_join(genes49DE, common1235.9,by="GENEID")
# genes59DE.r <- anti_join(genes59DE, common1235.9,by="GENEID")
# genes61DE.r <- anti_join(genes61DE, common1235.9,by="GENEID")
# genes76DE.r <- anti_join(genes76DE, common1235.9,by="GENEID")
# genes77DE.r <- anti_join(genes77DE, common1235.9,by="GENEID")
#find common DE genes in aneuploids with same chromosome aneuploid
# chrI.tri <- inner_join(genes7DE,genes18DE, by="GENEID")
# matchedI <- intersect(chrI.tri$GENEID, genes$GENEID)
# keepI <- chrI.tri$GENEID %in% matchedI
# chrI.tri <- chrI.tri[keepI,]
# keepGen <- genes$GENEID %in% matchedI
# Gen <- genes[keepGen,]
# chrI.tri <- cbind(Gen$TXCHROM, chrI.tri)
#
# chrI.all <- inner_join(chrI.tri, genes11DE, by="GENEID")
# matchedI <- intersect(chrI.all$GENEID, genes$GENEID)
# keepI <- chrI.all$GENEID %in% matchedI
# chrI.all <- chrI.all[keepI,]
#
# chrV.tri <- inner_join(genes4DE, genes49DE, by="GENEID")
# matchedV <- intersect(chrV.tri$GENEID, genes$GENEID)
# keepV <- chrV.tri$GENEID %in% matchedV
# chrV.tri <- chrV.tri[keepI,]
# keepGen <- genes$GENEID %in% matchedV
# Gen <- genes[keepGen,]
# chrV.tri <- cbind(Gen$TXCHROM, chrV.tri)
#
# chrVII.tri <- inner_join(genes59DE, genes61DE, by="GENEID")
# matchedVII <- intersect(chrVII.tri$GENEID, genes$GENEID)
# keepVII <- chrVII.tri$GENEID %in% matchedVII
# chrVII.tri <- chrVII.tri[keepVII,]
# keepGen <- genes$GENEID %in% matchedVII
# Gen <- genes[keepGen,]
# chrVII.tri <- cbind(Gen$TXCHROM, chrVII.tri)
#
# chrXII.tri <- inner_join(genes18DE, genes77DE, by="GENEID")
# matchedXII <- intersect(chrXII.tri$GENEID, genes$GENEID)
# keepXII <- chrXII.tri$GENEID %in% matchedXII
# chrXII.tri <- chrXII.tri[keepXII,]
# keepGen <- genes$GENEID %in% matchedXII
# Gen <- genes[keepGen,]
# chrXII.tri <- cbind(Gen$TXCHROM, chrXII.tri)
##any commonly DE genes between 2+ aneuploids?
#that are NOT commonly DE in euploid lines
# dupRows <- dupsBetweenGroups(allSamplesDE, "Sample")
#find any genes on aneuploid chromosomes that are NOT DE
# notDE4 <- subset(res4Dat,padj>0.1)
# notDE7 <- subset(res7Dat,padj>0.1)
# notDE8 <- subset(res8Dat,padj>0.1)
# notDE11 <- subset(res11Dat,padj>0.1)
# notDE18 <- subset(res18Dat,padj>0.1)
# notDE49 <- subset(res49Dat,padj>0.1)
# notDE59 <- subset(res59Dat,padj>0.1)
# notDE61 <- subset(res61Dat,padj>0.1)
# notDE76 <- subset(res76Dat,padj>0.1)
# notDE77 <- subset(res77Dat,padj>0.1)
# notDECom <- inner_join(notDE4, notDE7, by="GENEID")
# notDECom <- inner_join(notDECom, notDE8, by="GENEID")
# notDECom <- inner_join(notDECom, notDE11, by="GENEID")
# notDECom <- inner_join(notDECom, notDE18, by="GENEID")
# notDECom <- inner_join(notDECom, notDE49, by="GENEID")
# notDECom <- inner_join(notDECom, notDE59, by="GENEID")
# notDECom <- inner_join(notDECom, notDE61, by="GENEID")
# notDECom <- inner_join(notDECom, notDE76, by="GENEID")
# notDECom <- inner_join(notDECom, notDE77, by="GENEID")
summary(res4)
res7 <- results(ddsNoAneuInNorm, contrast=c("condition","Holly_7","Holly_Anc"))#,cooksCutoff=FALSE)
res7 <- results(ddsNoAneuInNorm, contrast=c("condition","Holly_7","Holly_Anc"))#,cooksCutoff=FALSE)
summary(res7)
View(res7)
avgRatio7 <- average(res7$log2FoldChange)
avgRatio7 <- mean(res7$log2FoldChange)
avgRatio7
avgRatio11 <- mean(res7$log2FoldChange)
avgRatio11
avgRatio11 <- mean(res11$log2FoldChange)
avgRatio11
avgRatio18 <- mean(res18$log2FoldChange)
avgRatio18
venn.plotChrI <- venn.diagram(
x = list(
A = deGenesNotAneuS7$GENEID,
B = deGenesNotAneuS18$GENEID,
C = deGenesNotAneuS11$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
grid.draw(venn.plotChrI)
grid.draw(venn.plotChrI)
venn.plotChrINonDE <- venn.diagram(
x = list(
A = nonDES11c1$GENEID,
B = nonDES18c1$GENEID,
C = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
grid.draw(venn.plotChrINonDE)
grid.draw(venn.plotChrINonDE)
pdf("commonNonDE_chrI.pdf")
venn.plotChrINonDE <- venn.diagram(
x = list(
A = nonDES11c1$GENEID,
B = nonDES18c1$GENEID,
C = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
pdf("commonNonDE_chrI.pdf")
dev.off()
venn.plotChrINonDE <- venn.diagram(
x = list(
A = nonDES11c1$GENEID,
B = nonDES18c1$GENEID,
C = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
pdf("commonNonDE_chrI.pdf")
pdf("commonNonDE_chrI.pdf")
grid.draw(venn.plotChrINonDE)
dev.off()
venn.plotChrINonDE <- venn.diagram(
x = list(
"11" = nonDES11c1$GENEID,
"18" =nonDES18c1$GENEID,
"7" = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
grid.draw(venn.plotChrINonDE)
grid.draw(venn.plotChrINonDE)
venn.plotChrINonDE <- venn.diagram(
x = list(
"L11" = nonDES11c1$GENEID,
"L18" =nonDES18c1$GENEID,
"L7" = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
grid.draw(venn.plotChrINonDE)
venn.plotChrINonDE <- venn.diagram(
x = list(
"L11" = nonDES11c1$GENEID,
"L18" =nonDES18c1$GENEID,
"L7" = nonDES7c1$GENEID
),
filename = NULL,
fill = c("orange", "deeppink1","turquoise"),
cex=2
)
pdf("commonNonDE_chrI.pdf")
grid.draw(venn.plotChrINonDE)
dev.off()
venn.plotChrINonDETris <- venn.diagram(
x = list(
"L18" =nonDES18c1$GENEID,
"L7" = nonDES7c1$GENEID
),
filename = NULL,
fill = c( "deeppink1","turquoise"),
cex=2
)
pdf("commonNonDE_chrITri.pdf")
grid.draw(venn.plotChrINonDETris)
dev.off()
View(triChrVIISamplesDiffExpr)
nonDES59c5$GENEID
chrVNon <- getCommonNonDEgenes(nonDES4c5, nonDES49c5)
View(chrVNon)
venn.plotChrVNonDE <- venn.diagram(
x = list(
"L4" =nonDES4c5$GENEID,
"L49" = nonDES49c5$GENEID
),
filename = NULL,
fill = c( "goldenrod","turquoise"),
cex=2
)
grid.draw(venn.plotChrVNonDE)
grid.draw(venn.plotChrVNonDE)
venn.plotChrVNonDE <- venn.diagram(
x = list(
"L4" =nonDES4c5$GENEID,
"L49" = nonDES49c5$GENEID
),
filename = NULL,
fill = c( "goldenrod","turquoise"),
cex=2
)
pdf("commonNonDE_chrVTri.pdf")
grid.draw(venn.plotChrVNonDE)
dev.off()
chrVNon <- getCommonNonDEgenes(nonDES4c5, nonDES49c5)
View(chrVNon)
write.csv(chrVNon, file="chrVallDNonE_GC.csv")