runMetaGene: Runs metagene analysis for sense and antisense direction.

In groHMM: GRO-seq Analysis Pipeline

Description

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, set the option 'mc.cores'.

Usage

runMetaGene(features, reads, anchorType = "TSS", size = 100L,
  normCounts = 1L, up = 10000L, down = NULL, sampling = FALSE,
  nSampling = 1000L, samplingRatio = 0.1, ...)

Arguments

features	GRanges A GRanges object representing a set of genomic coordinates, i.e., set of genes.
reads	GRanges of reads.
anchorType	Either 'TSS' or 'TTS'. Metagene will be centered on the transcription start site(TSS) or transcription termination site(TTS). Default: TSS.
size	Numeric. The size of the moving window. Default: 100L
normCounts	Numeric. Normalization vector such as average reads. Default: 1L
up	Numeric. Distance upstream of each feature to align and histogram. Default: 1 kb
down	Numeric. Distance downstream of each feature to align and histogram. If NULL, down is same as up. Default: NULL
sampling	Logical. If TRUE, subsampling of Metagene is used. Default: FALSE
nSampling	Numeric. Number of subsampling. Default: 1000L
samplingRatio	Numeric. Ratio of sampling for features. Default: 0.1
...	Extra argument passed to mclapply.

Value

A list of integer-Rle for sense and antisene.

Author(s)

Minho Chae

Examples

features <- GRanges("chr7", IRanges(start=1000:1001, width=rep(1,2)),
 strand=c("+", "-"))
reads <- GRanges("chr7", IRanges(start=c(1000:1003, 1100:1101),
 width=rep(1, 6)), strand=rep(c("+","-"), 3))
## Not run:
# mg <- runMetaGene(features, reads, size=4, up=10)

groHMM documentation built on Nov. 8, 2020, 8:09 p.m.