Runs metagene analysis for sense and antisense direction.

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Description

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

Usage

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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

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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)

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