est_r_m {erccdashboard} | R Documentation

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

### 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)

[Package erccdashboard version 1.12.1 Index]