APAdiff: APAdiff, calculate delta relative expression (RED) and...

In RJWANGbioinfo/APAlyzer: A toolkit for APA analysis using RNA-seq data

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", MultiTest='unpaired t-test')

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"
MultiTest	statistics testing method for muti-replicates designs, the method can be "unpaired t-test", "paired t-test", "ANOVA", default is "unpaired t-test"

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",MultiTest='unpaired t-test')

    ## 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",MultiTest='unpaired t-test')

    ## 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")

RJWANGbioinfo/APAlyzer documentation built on Dec. 6, 2024, 3:36 p.m.