plotVmat.GRanges.RdA function to plot a computed Vmat
# S3 method for GRanges plotVmat(bam_granges, granges, XAXIS.CUTOFF = 1000, YAXIS.CUTOFF = 1000, stranded = TRUE, normalize = TRUE, Vmat2 = NULL, estimate_background = TRUE, background_granges = NULL, normFun = "pctsum", roll = 3, return_Vmat = FALSE, genome = "ce11", ...)
| bam_granges | GRanges. The paired-end fragments |
|---|---|
| granges | GRanges. The regions to map the fragments onto |
| XAXIS.CUTOFF | single integer. The x limits (-/+) of the computed Vmat |
| YAXIS.CUTOFF | single integer. The y upper limit of the computed Vmat |
| stranded | Boolean. Should the Vmat be stranded? If TRUE, negative-strand features are flipped |
| normalize | Boolean Should the Vmat be normalized? |
| Vmat2 | table A Vmat pre-computed over a background |
| estimate_background | Boolean Should the background be estimated automatically? |
| background_granges | GRanges The genomic loci used to compute the background Vmat |
| normFun | string A Vmat can be scaled relative to its median ('pctmedian'), to its mean ('pctmean'), to its max ('pctmax'). Otherwise it could be zscore-d entirely ('Zscore') or by rows ('rowZscore') or by columns ('colZscore'). |
| roll | integer to use as the window to smooth the Vmat rows by rolling mean |
| return_Vmat | Boolean. Should the function return the computed Vmat rather than the plot? |
| genome | a BSgenome object. See getChromSizes for more details |
A Vmat ggplot