runMetaGene: Runs meta gene analysis for sense and anti-sense direction.

Description Usage Arguments Value Author(s) Examples

Description

Runs meta gene analysis for sense and anti-sense direction.

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, BPPARAM = bpparam())

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'. Meta gene 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, sub-sampling of meta gene is used. Default: FALSE

nSampling

Numeric. Number of sub-sampling. Default: 1000L

samplingRatio

Numeric. Ratio of sampling for features. Default: 0.1

BPPARAM

Registered backend for BiocParallel. Default: BiocParallel::bpparam()

Value

A list of integer-Rle for sense and anti-sense.

Author(s)

Minho Chae

Examples

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library(GenomicRanges)
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)

omsai/groHMM documentation built on May 24, 2019, 2:18 p.m.