R: RaMWAS: High Level Pipeline Functions

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

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]