ramwasParameters {ramwas} | R Documentation |
RaMWAS parameter vector which is used by major functions of the pipeline is a regular R list and setting it does not require a special function. However, using this function makes it much simpler in RStudio as the names and role of every parameter is showed in the RStudio IDE.
ramwasParameters( dirproject, dirfilter, dirrbam, dirrqc, dirqc, dircoveragenorm, dirtemp, dirpca, dirmwas, dircv, dirbam, filebamlist, bamnames, filebam2sample, bam2sample, filecpgset, filenoncpgset, filecovariates, covariates, cputhreads, diskthreads, usefilelock, scoretag, minscore, maxrepeats, minavgcpgcoverage, minnonzerosamples, buffersize, doublesize, modelcovariates, modeloutcome, modelPCs, modelhasconstant, qqplottitle, toppvthreshold, mmncpgs, mmalpha, cvnfolds, bihost, bimart, bidataset, biattributes, bifilters, biflank, fileSNPs, dirSNPs, ...)
dirproject |
The project directory. Default is currect directory. |
dirfilter |
By default, the same as "dirproject". |
dirrbam |
Directory where RaMWAS saves RaMWAS raw data files
(read start locations) after scanning BAMs. |
dirrqc |
Directory where RaMWAS saves QC files in R format after scanning BAMs.
|
dirqc |
Directory where RaMWAS saves QC plots and text files (BAM QC info)
after scanning BAMs. |
dircoveragenorm |
Directory where RaMWAS saves coverage matrix at Step 3 of the pipeline.
|
dirtemp |
Directory where RaMWAS stores temporary files
during construction of coverage matrix at Step 3 of the pipeline. |
dirpca |
Directory where RaMWAS saves results of PCA analysis at Step 4
of the pipeline. |
dirmwas |
Directory where RaMWAS saves results of MWAS analysis at Step 5
of the pipeline. |
dircv |
Directory where RaMWAS saves results of Methylation Risk Score analysis
at Step 7 of the pipeline. |
dirbam |
Location of BAM files. |
filebamlist |
If defined, must point to a text file with one BAM file name per line.
|
bamnames |
A character vector with BAM file names. |
filebam2sample |
Allowes multiple BAMs contain information about common sample. |
bam2sample |
Allowes multiple BAMs contain information about common sample. |
filecpgset |
Name of the file storing a set of CpGs. |
filenoncpgset |
If defined, must point to a file storing vetted locations away from any CpGs. |
filecovariates |
Name of the file containing phenotype and covariates
for the available samples. |
covariates |
Data frame with phenotype and covariates
for the available samples. |
cputhreads |
Maximum number of CPU intensive tasks running in parallel. |
diskthreads |
Maximum number of disk intensive tasks running in parallel. |
usefilelock |
If TRUE, parallel jobs are prevented from simultaneous access
to file matrices. |
scoretag |
Reads from BAM files are filtered by this tag. |
minscore |
Reads from BAM files with score "scoretag" below this are excluded. |
maxrepeats |
Duplicate reads (reads with the same start position and direction) in excess of this limit are removed. |
minavgcpgcoverage |
CpGs with average coverage below this threshold are removed. |
minnonzerosamples |
CpGs with fraction of samples with non-zero coverage below this threshold are removed. |
buffersize |
Coverage matrix transposition is performed using buffers of this size.
|
doublesize |
The coverage matrix is stored with this number of bytes per value. |
modelcovariates |
Names of covariates included in PCA and MWAS. |
modeloutcome |
Name of the outcome variable for MWAS. |
modelPCs |
Number of principal components accounted for in MWAS. |
modelhasconstant |
By default, the tested linear model includes a constant. |
qqplottitle |
The title of the QQ-plot produced by MWAS (step 4 of the pipeline). |
toppvthreshold |
Determines the number of top MWAS results saved in text file. |
mmncpgs |
Parameter for multi-marker elastic net cross validation (MRS). |
mmalpha |
Parameter for multi-marker elastic net cross validation (MRS). |
cvnfolds |
Parameter for multi-marker elastic net cross validation (MRS). |
bihost |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
bimart |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
bidataset |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
biattributes |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
bifilters |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
biflank |
Parameter for BiomaRt annotation (Step 6 of the pipeline). |
fileSNPs |
Name of the filematrix with genotype (SNP) data. |
dirSNPs |
Directory where RaMWAS saves the results of joint methylation-genotype analysis. |
... |
Any other named parameters can be added here. |
The function simply collects all the parameters in a list.
The main benefit of the function is that the user does not
need to memorize the names of RaMWAS parameters.
Here is how it helps in RStudio:
List with provided parameters.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
ramwasParameters(dirproject = ".", cputhreads = 4)