ProcessOutputFilesFrom3UTR: ProcessOutputFilesFrom3UTR

In aiminy/3UTR-Seq: An R package for processing and analyzing 3UTR,DOGs and 5UTR data

Description

read the mapping results from the Dogs of each gene

Usage

ProcessOutputFilesFrom3UTR(dir.name, input.file.pattern, normal.factor, out)

Arguments

dir.name:	the path for input files
input.file.pattern:	input file pattern

Examples

dir.name="/media/H_driver/2016/Ramin_azhang/for_bioinfo_core/RNA_seq/Results/"

#new data
dir.name="/media/H_driver/2016/Ramin_azhang/for_bioinfo_core/RNA_seq/Results4NewData/"
input.file.pattern="*downstream.count.hg19.strand.based.txt"

com.input.file.pattern="*downstream.com.count.hg19.strand.based.txt"

total.com.input.file.pattern="*.gene.downstream.count.hg19.strand.based.total2.txt"

#use intergenic reads as normal factor
normal.factor="*.rm.exon.intron.hg19.bed"

#use total reads as normal factor
normal.factor="*.bed"

sink("testcode.txt")
re.rMAT<-ProcessOutputFilesFrom3UTR(dir.name,input.file.pattern,normal.factor,"intergenic")
re.rMAT.com<-ProcessOutputFilesFrom3UTR(dir.name,com.input.file.pattern,normal.factor,"com_intergenic")

re.rMAT.com.total<-ProcessOutputFilesFrom3UTR(dir.name,total.com.input.file.pattern,normal.factor,"com_total")

re.rMAT.com.total.interested<-re.rMAT.com.total$DE[which(re.rMAT.com.total$DE$gene %in% genes.interested[,1]),]

re.com.total.pos<-re.rMAT.com.total.interested[which(re.rMAT.com.total.interested$`FoldChange(WT/Dox)`<1),]
re.com.total.neg<-re.rMAT.com.total.interested[which(re.rMAT.com.total.interested$`FoldChange(WT/Dox)`>=1),]


re.com.total.pos[which(re.com.total.pos$gene %in% c("TPCN2")),]

re.rMAT.com.interested<-re.rMAT.com$DE[which(re.rMAT.com$DE$gene %in% genes.interested[,1]),]
re.pos<-re.rMAT.com.interested[which(re.rMAT.com.interested$`FoldChange(WT/Dox)`<1),]
re.neg<-re.rMAT.com.interested[which(re.rMAT.com.interested$`FoldChange(WT/Dox)`>=1),]


re.rMAT.total<-ProcessOutputFilesFrom3UTR(dir.name,input.file.pattern,normal.factor,"total")
re.rMAT.com.total<-ProcessOutputFilesFrom3UTR(dir.name,com.input.file.pattern,normal.factor,"com_total")

sink()

sink("test_com_total.txt")
re.rMAT.com.total.test<-ProcessOutputFilesFrom3UTR(dir.name,com.input.file.pattern,normal.factor,"com_total_test")
sink()

re.rMAT.com.total.test.2<-ProcessOutputFilesFrom3UTR(dir.name,total.com.input.file.pattern,normal.factor,"com_total_test_3")

geoMeans <- exp(rowMeans(log(counts(re.rMAT.com.total.test$dds))))

temp.dds<-re.rMAT.com.total.test.2$dds

normalizationFactors(temp.dds)
size..factor<-estimateSizeFactors(re.rMAT.com.total.test$dds,geoMeans=geoMeans)
sizeFactors(size..factor)

temp.dds <- estimateSizeFactors(temp.dds)

count.norm<-counts(temp.dds,normalized = TRUE)

head(count.norm)

DE.norm.with.rpkm.norm<-cbind(count.norm,re.rMAT.com.total.test.2$MergedNorma[,c(1,3,7,11,13,5,9,15,17)])

DE.norm.with.rpkm.norm.2<-DE.norm.with.rpkm.norm[,-9]

col.name<-c(paste0("D.",sapply(strsplit(colnames(DE.norm.with.rpkm.norm.2)[1:8],"\\."),"[[",2)),
paste0("R.",sapply(strsplit(colnames(DE.norm.with.rpkm.norm.2)[9:16],"\\."),"[[",3)))

col.name.2<-gsub("2016-02-10-","",col.name)

cbind(colnames(DE.norm.with.rpkm.norm.2),col.name.2)

colnames(DE.norm.with.rpkm.norm.2)<-col.name.2


DE.norm.with.rpkm.norm.3<-apply(DE.norm.with.rpkm.norm.2,2,as.numeric)

par(mfrow = c(4, 2))  # 3 rows and 2 columns
for (i in 1:8) {
plot(DE.norm.with.rpkm.norm.3[,c(i,i+8)])
model <- lm(DE.norm.with.rpkm.norm.3[,i+8] ~ DE.norm.with.rpkm.norm.3[,i], data = as.data.frame(DE.norm.with.rpkm.norm.3))
abline(model, col = "red")
}

plot(apply(DE.norm.with.rpkm.norm.2,2,as.numeric)[,1:3])

M <- cor(DE.norm.with.rpkm.norm.3[,1:8])

corrplot.mixed(M)

corrplot(M,method="ellipse",order = "hclust", addrect = 2)

corrplot(M,method="number",order = "hclust", addrect = 2)

corrplot(M,method="number",order = "FPC", addrect = 2)

corrplot(M,method="ellipse")

corrplot(M,method="ellipse",type="upper",)
corrplot(M, method="number")

corrplot(M,method="ellipse",order="hclust", addrect=4)

size.factor.2<-estimateSizeFactors(re.rMAT.com.total.test.2$dds)
sizeFactors(size.factor.2)

aiminy/3UTR-Seq documentation built on May 10, 2019, 7:36 a.m.