pipeline {ramwas} | R Documentation |
These functions provide a simple way to run all steps of RaMWAS pipeline.
ramwas1scanBams(param) pipelineProcessBam(bamname, param) ramwas2collectqc(param) ramwas3normalizedCoverage(param) ramwas4PCA(param) ramwas5MWAS(param) ramwas6annotateTopFindings(param) ramwas7ArunMWASes(param) ramwas7BrunElasticNet(param) ramwas7CplotByNCpGs(param) ramwas7riskScoreCV(param) ramwasSNPs(param)
param |
List with RaMWAS parameters. |
bamname |
Name of the BAM file to process.
Can be absolute or relative to |
See vignettes for details: browseVignettes("ramwas")
.
Function pipelineProcessBam
returns "OK. <bamname>"
if no error occurred. Otherwise, returns text with error.
Other functions return nothing.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
param = ramwasParameters( dirbam = "/project/bams", dirproject = "/project", filebamlist = "000_list_of_files.txt", scoretag = "AS", minscore = 100, cputhreads = 4, filecpgset = "/RaMWAS/hg19_1kG_MAF_0.01_chr1-22_bowtie2_75bp.rds", filenoncpgset = "/RaMWAS/hg19_1kG_MAF_0.01_chr1-22_bowtie2_75bp_nonCpG.rds", maxrepeats = 3, maxfragmentsize = 250, minfragmentsize = 75, filebam2sample = "000_list_of_files.txt", filecovariates = "Covariates.txt", modelcovariates = c("Age","Sex"), modeloutcome = "CellType", modelPCs = 1, cvnfolds = 10, mmncpgs = 1000, mmalpha = 0 ) ## Not run: ramwas1scanBams(param) ramwas2collectqc(param) ramwas3normalizedCoverage(param) ramwas4PCA(param) ramwas5MWAS(param) ramwas6annotateTopFindings(param) ramwas7riskScoreCV(param) ## End(Not run)