mergeBatches: Merges data from several batches for cohort analysis

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

Merges data from several batches for cohort analysis

Description

Merges data from several batches for cohort analysis

Usage

mergeBatches(paths, targetMetaDataFile, targetRdirectory, cpus = 1)

Arguments

paths	data.frame: One row for each batch to be merged.
targetMetaDataFile	character: Path to where the merged metaData will be stored. This also affect where a downstream cohort analysis is stored.
targetRdirectory	character: Path to where the Rdata will be stored.

Details

This function merges the data from multiple batches, setting them up for a joint cohort analysis. Note that this is only for the purpose of a downstream cohort analysis. The output R directory cannot be run as a batch Rdirectory.

Examples

## Not run: 
paths = data.frame('metaDataFile' = c('~/superFreq/myFirstBatch/metaData.txt', '~/superFreq/mySecondBatch/metaData.txt'),
           'Rdirectory'= c('~/superFreq/myFirstBatch/R', '~/superFreq/myFirstBatch/R'))

targetMetaDataFile = '~/superFreq/mergedAnalysis/metaData.txt'
targetRdirectory = '~/superFreq/mergedAnalysis/R'

mergeBatches(paths, targetMetaDataFile, targetRdirectory)

outputDirectories = list('Rdirectory'=targetRdirectory)
cohortAnalyseBatch(targetMetaDataFile, outputDirectories, cpus=6, genome='hg19')


## End(Not run)

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.