RnaSeqSampleSize (version 1.4.2)

est_count_dispersion: est_count_dispersion

Description

A function to estitamete the gene read count and dispersion distribution of RNA-seq data.

Usage

est_count_dispersion(counts, group = rep(1, NCOL(counts)), subSampleNum = 20, minAveCount = 1, convertId = FALSE, dataset = "hsapiens_gene_ensembl", filters = "hgnc_symbol")

Arguments

counts

numeric matrix of read counts.

group

vector or factor giving the experimental group/condition for each sample/library.

subSampleNum

number of samples used to estitamete distribution.

minAveCount

Only genes with avarage read counts above this value are used in the estimation of distribution.

convertId

logical, whether to convert th gene Id into entrez gene Id. If set as True, then dataset and filters parameter should also be set.

dataset

Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart).

filters

Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function listFilters.

Value

A DEGlist from edgeR package.

Details

A function to estitamete the gene read count and dispersion distribution of RNA-seq data.

Examples

counts<-matrix(sample(1:1000,6000,replace=TRUE),ncol=6)
est_count_dispersion(counts=counts,group=rep(0,6))