gene_expr_sum: Sum transcription expression estimates to gene-level...

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

Sum transcription expression estimates to gene-level expression measures

Description

Sums all trnascript level expression estimates to a single gene level estimate. Needs a table that maps transcript IDs to gene IDs.

Usage

gene_expr_sum(expDatList, numCores = 10,
  geneTabfname = "/media/ephemeral1/dat/ref/geneToTrans_Mus_musculus.GRCm38.80.exo_Jun_02_2015.R",
  nameCol = "gene_name")

Arguments

expDatList	result of running salmon_load_tranEst
numCores	num of cores to use for parallel
geneTabfname	gene <-> transcript mapping, df that needs cols: gene_id, transcript_id
nameCol	gene ann table column name to average over

Value

list(TPM=ansTPM, counts=ansCounts);

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