cn_salmon: Derive gene expression estimates compatible with CellNet

In pcahan1/CellNet: Assess and improve cell fate engineering with network biology

Derive gene expression estimates compatible with CellNet

Description

Derive gene expression estimates compatible with CellNet

Usage

cn_salmon(sampTab, total = 1e+05, fnameCol = "fname",
  finalLength = 40, delOrig = FALSE,
  salmonIndex = "MM_GRCh38.SalmonIndex.030816",
  geneTabfname = "geneToTrans_Mus_musculus.GRCm38.80.exo_Jun_02_2015.R",
  refDir = "/media/ephemeral1/dat/ref/",
  salmonPath = "~/rnaseq/SalmonBeta-0.6.1_DebianSqueeze/bin")

Arguments

sampTab	sample table with fname column point to fastq files
total	number of reads to normalzie to
fnameCol	column name of fastq files
finalLength	length of reads after trimming
species	mouse or human
bucket	where to get them
what	path on s3 to get them

Value

nothing

pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.