Usage
TrioSetListLD(path, fnames, ext = "", samplesheet, row.names, pedigreeData, featureData, annotationPkg, outdir = ldPath(), ffprefix = "", genome = c("hg19", "hg18"))
Arguments
path
Path to plain-text files containing log R ratios and B
allele frequencies. Files should contain data for a single sample.
fnames
Character string providing filenames.
ext
Character string indicating whether the fnames
has a file extension (e.g., ".txt")
samplesheet
(Optional) data.frame containing
phenotypic / experimental covariates on the samples. Note that if
samplesheet is provided, row.names must be specified.
row.names
Character vector indicating the sample id for each
row in samplesheet. row.names should be unique and,
ideally, correspond to fnames
pedigreeData
An object of class Pedigree.
featureData
A GenomeAnnotatedDataFrame
annotationPkg
Character string indicating the annotation
package used to extract information on the features (chromosome,
physical position, and whether the feature is polymorphic
('isSnp')).
outdir
Character string indicating the path for storing ff objects. Ignored if the ff package is not loaded.
ffprefix
Character string indicating the prefix used to name
ff objects. Ignored if the ff package is not loaded.
genome
character string indicating UCSC genome build. Only
"hg19" is allowed for annotation packages that support a single
build. Supported builds for most platforms are "hg18" and "hg19".