pipeline {ramwas}R Documentation

RaMWAS: High Level Pipeline Functions

Description

These functions provide a simple way to run all steps of RaMWAS pipeline.

Usage

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)

Arguments

param

List with RaMWAS parameters.
For detailed description of all available parameters run:
browseVignettes("ramwas").

bamname

Name of the BAM file to process. Can be absolute or relative to dirbam parameter (in param list).

Details

See vignettes for details: browseVignettes("ramwas").

Value

Function pipelineProcessBam returns "OK. <bamname>" if no error occurred. Otherwise, returns text with error. Other functions return nothing.

Author(s)

Andrey A Shabalin andrey.shabalin@gmail.com

See Also

See vignettes: browseVignettes("ramwas").

Examples

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)

[Package ramwas version 1.6.0 Index]