plotGeneCoverage: plotGeneCoverage
In scottzijiezhang/RADAR: RADAR

plotGeneCoverage

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plotGeneCoverage(IP_BAMs, INPUT_BAMs, size.IP, size.INPUT, X, geneName,
  geneModel, libraryType = "opposite", center = mean, GTF,
  ZoomIn = NULL, adjustExprLevel = "none", plotSNP = NULL)

`size.IP`	The size factor for IP libraries
`size.INPUT`	The size factor for INPUT libraries
`geneName`	The name (as defined in gtf file) of the gene you want to plot
`geneModel`	The gene model generated by gtfToGeneModel() function
`libraryType`	"opposite" for mRNA stranded library, "same" for samll RNA library
`GTF`	gtf annotation as GRanges object. Can be obtained by GTF <- rtracklayer::import("xxx.gtf",format = "gtf")
`adjustExprLevel`	A size factor representing the pre-IP expression level
`plotSNP`	The option to plot SNP on the figure. Null by default. If want to include SNP in the plot, the parameter needs to ba a dataframe like this: data.frame(loc= position, anno="A/G")
`IP_BAM`	The bam files for IP samples
`INPUT_BAM`	The bam files for INPUT samples