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]