est_r_m: Estimate the mRNA fraction differences for the pair of...

In erccdashboard: Assess Differential Gene Expression Experiments with ERCC Controls

Description

Estimate the mRNA fraction differences for the pair of samples using replicate data

Usage

est_r_m(exDat)

Arguments

exDat

list, contains input data and stores analysis results

Details

This is the first function to run after an exDat structure is initialized using initDat, because it is needed for all additional analysis. An r_m of 1 indicates that the two sample types under comparison have similar mRNA fractions of total RNA. The r_m estimate is used to adjusted the expected ERCC mixture ratios in this analysis and may indicate a need for a different sample normalization approach.

Examples

data(SEQC.Example)

exDat <- initDat(datType="count", isNorm = FALSE, exTable=MET.CTL.countDat, 
                 filenameRoot = "testRun",sample1Name = "MET",
                 sample2Name = "CTL", erccmix = "RatioPair", 
                 erccdilution = 1/100, spikeVol = 1, totalRNAmass = 0.500,
                 choseFDR = 0.1)

exDat <- est_r_m(exDat)

erccdashboard documentation built on Nov. 8, 2020, 5:50 p.m.