est_r_m {erccdashboard} | R Documentation |
Estimate the mRNA fraction differences for the pair of samples using replicate data
est_r_m(exDat)
exDat |
list, contains input data and stores analysis results |
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.
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)