est_count_dispersion: est_count_dispersion

In slzhao/RnaSeqSampleSize: RnaSeqSampleSize

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.

Details

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

Value

A DEGlist from edgeR package.

Examples

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

slzhao/RnaSeqSampleSize documentation built on March 24, 2022, 2:21 a.m.