degall: Differential Expression analysis using all combination In shkonishi/rskoseq: This is my personal package of R functions for NGS data

Description

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

Usage

 `1` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19``` ```## 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 Sept. 11, 2018, 12:39 a.m.