TrioSetListLD: Deprecated TrioSetList constructor for large data

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Description

The TrioSetListLD constructor uses ff objects to handle large datasets. This function is defunct. Use MinDistExperiment instead.

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".

Value

A TrioSetList object

See Also

TrioSetList

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.