metaGene {groHMM} | R Documentation |
Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, set the option 'mc.cores'.
metaGene(features, reads = NULL, plusCVG = NULL, minusCVG = NULL, size = 100L, up = 10000L, down = NULL, ...)
features |
A GRanges object representing a set of genomic coordinates. The meta-plot will be centered on the transcription start site (TSS) |
reads |
A GRanges object representing a set of mapped reads. Instead of 'reads', 'plusCVG' and 'minusCVG' can be used Default: NULL |
plusCVG |
An IntegerRangesList object for reads with '+' strand. |
minusCVG |
An IntegerRangesList object for reads with '-' strand. |
size |
The size of the moving window. |
up |
Distance upstream of each features to align and histogram. Default: 10 kb. |
down |
Distance downstream of each features to align and histogram. If NULL, same as up. Default: NULL. |
... |
Extra argument passed to mclapply |
Returns a integer-Rle representing the 'typical' signal centered on a point of interest.
Charles G. Danko and Minho Chae
features <- GRanges("chr7", IRanges(1000, 1000), strand="+") reads <- GRanges("chr7", IRanges(start=c(1000:1004, 1100), width=rep(1, 6)), strand="+") mg <- metaGene(features, reads, size=4, up=10)