toDESeq2: RepSeqCount to DESeqDataSet

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function transforms a RepSeqCount object to an DESeqDataSet object

Usage

toDESeq2(x, conditions, level = c("VpJ", "V", "J", "VJ", "CDR3aa"))

Arguments

x	an object of class RepSeqExperiment
conditions	name(s) of column(s) in sample information (sData(x)) defining test between biological conditions.
level	of repertoire to analyze VpJ, VJ, V, J, CDR3aa.

Value

a DESeqDataSet object

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeqData)
sData(RepSeqData)
dds <- toDESeq2(x = RepSeqData, conditions = "project" , level = "VJ")
dds

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.