processSRA: processes a SRA study

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

processes a SRA study

Description

This function is a wrapper to qcAndSalmon. It also summarizes transcript into gene expression estimates

Usage

processSRA(sampTab, inc = 5, studyID = NA, bucket = "cellnet-rnaseq",
  startDir = "singlecell", finalLength = 40, subProp = 0.001,
  target = "mouse",
  gtfFile = "/media/ephemeral1/dat/ref/Mus_musculus.GRCm38.83.gtf",
  geneTabfname = "/media/ephemeral1/dat/ref/geneToTrans_Mus_musculus.GRCm38.80.exo_Jun_02_2015.R",
  salmonIndex = "/media/ephemeral1/dat/ref/MM_GRCh38.SalmonIndex.030816")

Arguments

sampTab	sample table
inc	increment size
studyID	study id
bucket	S3 bucket where to put the results
startDir	S3 bucket path to store results
finalLength	final length of reads
subProp	proportion of reads to sample from for QC
target	species/genome for expression estimates
gtfFile	genomic feature of target genome for QC
geneTabfname	transcript <-> gene data frame
salmonIndex	path to salmon index for expression estimation

Value

sample table with QC measures appened. side effect is storage of expression estimates + sample table to S3

Examples

processSRA(stX, inc=5)

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