APAdiff {APAlyzer} | R Documentation

## APAdiff, calculate delta relative expression (RED) and statistics significance between two sample groups

### Description

Calculate delta relative expression (RED) and statistics significance between two sample groups.

### Usage

        APAdiff(sampleTable,mutiraw, conKET='NT',
        trtKEY='KD',PAS='3UTR',CUTreads=0,p_adjust_methods="fdr")

### Arguments

`sampleTable` | a dataframe of sample table containing 8 colmuns for Intronic PASs: 'samplename','condition'
`mutiraw` | a dataframe output obtained using either PASEXP_3UTR or PASEXP_IPA
`conKET` | the name of control in the sampletable, default is 'NT'
`trtKEY` | the name of control in the sampletable, default is 'KD'
`PAS` | type of PAS analyzed, either '3UTR' or 'IPA', default is '3UTR'
`CUTreads` | reads cutoff used for the analysis, default is 0
`p_adjust_methods` | p value correction method, the method can be "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none", default is "fdr"

### Value

The function `APAdiff` return a dataframe containning RED, pvalue and regulation pattern (UP, DN or NC) for either each gene (3'UTR APA) or each PAS (IPA).

### Author(s)

Ruijia Wang

### Examples

        library("TBX20BamSubset")
        library("Rsamtools")
        flsall = getBamFileList()
        extpath = system.file("extdata",
        "mm9_TBX20.APAout.RData", package="APAlyzer")
        load(extpath)
        sampleTable1 = data.frame(samplename = c(names(flsall)),
            condition = c(rep("NT",3),rep("KD",3)))
        sampleTable2 = data.frame(samplename = c("SRR316184","SRR316187"),
            condition = c("NT","KD"))
        ## Analysis 3'UTR APA between KD and NT group using muti-replicates
        test_3UTRmuti=APAdiff(sampleTable1,DFUTRraw,
        conKET='NT',trtKEY='KD',PAS='3UTR',CUTreads=0,p_adjust_methods="fdr")

        ## Analysis 3'UTR APA between KD and NT group without replicates
        test_3UTRsing=APAdiff(sampleTable2,DFUTRraw,
        conKET='NT',trtKEY='KD',PAS='3UTR',CUTreads=0,p_adjust_methods="fdr")

        ## Analysis IPA between KD and NT group
        test_IPAmuti=APAdiff(sampleTable1,IPA_OUTraw,
        conKET='NT',trtKEY='KD',PAS='IPA',CUTreads=0,p_adjust_methods="fdr")

        ## Analysis IPA between KD and NT group without replicates
        test_IPAsing=APAdiff(sampleTable2,IPA_OUTraw,
        conKET='NT',trtKEY='KD',PAS='IPA',CUTreads=0,p_adjust_methods="fdr")

[Package APAlyzer version 1.8.0 Index]