pipeline: RaMWAS: High Level Pipeline Functions

In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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 [e-mail]

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)

andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.