plotTopTags: Coverage plots

In estepi/ASpli: Analysis of alternative splicing using RNA-Seq

Description

Using genomic coordinates and BAM files this function is useful for make coverage plots

Usage

plotTopTags(auxdf, genome, targetsPlot, output.dir)

Arguments

auxdf	A data frame: row.naMes=bin names, gene coordinates, bin coordinates and event name columns
genome	TxDb genome
targetsPlot	A dataframe containting: bam files name, condition (y axe tag), color for each condition
output.dir	Name of directory where plots are supossed to be exported

Value

Coverage plots in png format of selected events

Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

Examples

library(RNAseqData.HNRNPC.bam.chr14)
chr14 <- system.file("extdata","chr14.sqlite", package="ASpli")
genome <- loadDb(chr14)
features <- binGenome(genome) 
targets <- data.frame(bam=RNAseqData.HNRNPC.bam.chr14_BAMFILES,
                       condition=c(rep("CT",4),rep("KD",4)))
bam <- loadBAM(targets)
counts <- readCounts(features, bam, l=100L, maxISize = 50000)
pair <- c("CT","KD")
group <- c(rep("CT", 4),rep("KD", 4))
du_HNRNPC <- DUreport(counts, targets, pair, group)  
bins <- binsDU(du_HNRNPC)
topTagsBins <- which(bins$bin.fdr <= 0.1 & 
                     abs(bins$logFC) >=0.58)
targetsPlot <- data.frame(bam=targets$bam, 
                        sample=targets$condition, 
                        color=c(rep("blue", 4),rep("red", 4)), 
                        stringsAsFactors=FALSE)

auxdf<-bins[topTagsBins,]
#for simplicity, just one: LRR1:E005

plotTopTags(auxdf["LRR1:E005",], 
            genome, 
            targetsPlot, 
            output.dir="testPlots")

estepi/ASpli documentation built on May 16, 2019, 8:53 a.m.