file2dds: Building DESeqDataSet

In xuzhougeng/zgtools: Xu Zhougeng's Toolkits

Description

file2dds build DESeqDataSet base on a vector input of sample file path, its counter and experiment design for use of DESeq2

Usage

file2dds(filepath, type, colData, design, txDb = NULL, keyType = "GENEID",
  column = "TXNAME", ...)

Arguments

filepath	a vector of file path of gene count
type	method to count gene, one of HTSeq, Salmon, Sailfish, kallisto
colData	a data.frame containning sample information with columns of sample name, treatment
design	a formula which expresses how the counts for each gene depend on the variables in colData. Many R formula are valid, e.g, ~ group, ~ group + condition, ~genotype + treatment + genotype: treatment.
txDb	a GenomicFeatures object, which could be downloaded from AnnotationHub.
...	other paramter from tximport

Value

DESeqDataSet object

xuzhougeng/zgtools documentation built on May 4, 2019, 4:23 p.m.