degall: Differential Expression analysis using all combination

Description Usage Arguments Value Examples

View source: R/degall.R

Description

split count data with index and Differential expression analysis of all comination groups.

Usage

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degall(dat, idx, normalize)

Arguments

dat

dataframe: RNA-seq count table. row: samples, column: genes

idx

factor: group of data. E.g. factor(c(1,1,2,2)); factor(c("A","A","B","B"))

normalize

integer: If dat is already normalized count data, 'norm' is NULL. The default value is NULL If dat is not normalized, select a pipe line number from 1:"DEGES/TbT", 2:"DEGES/edgeR", 3:"DEGES/DESeq".

Value

ggplot object which containing result of 'TCC::estimateDE', without normalized count data.

Examples

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## normalized fpkm
# nfpkm <- rskodat::nfpkm[c(1:3, 10:12, 19:21, 28:30),]
# index <- factor(rep(1:4, each=3))
# res <- rskoseq::degall(dat=nfpkm[-1:-4], idx=index, normalize=NULL)

## get result of estimateDE
# head(res$data)

## MA-plot
# ggplus::facet_multiple(res, facets="comp", ncol = 3, nrow = 5)

## single comparison
# comp1 <- nfpkm[nfpkm$days =="d3" & nfpkm$runs %in% c("S1", "S2"),]
# comp2 <- nfpkm[nfpkm$days =="d6" & nfpkm$runs %in% c("S1", "S2"),]
# comp3 <- nfpkm[nfpkm$days =="d12" & nfpkm$runs %in% c("S1", "S2"),]
# index <- factor(rep(1:2, each=3))
# res1 <- rskoseq::degall(dat=comp1[-1:-4], idx=index, normalize=NULL)
# res2 <- rskoseq::degall(dat=comp2[-1:-4], idx=index, normalize=NULL)
# res3 <- rskoseq::degall(dat=comp3[-1:-4], idx=index, normalize=NULL)

shkonishi/rskoseq documentation built on June 24, 2018, 6:19 a.m.