read_idats: Efficiently import idats files mostly using minfi functions.

In omicsr/dmapaq: DNA Methylation Arrays Processing And Quality-Control

Description

Efficiently import idats files mostly using minfi functions.

Usage

read_idats(
  directory = getwd(),
  csv_file = "csv$",
  meth_value_type = "B",
  filter_beads = TRUE,
  bead_cutoff = 0.05,
  filter_non_cpg = TRUE,
  filter_snps = TRUE,
  population = NULL,
  filter_multihit = TRUE,
  filter_xy = TRUE,
  detection_pvalues = 0.01,
  filter_callrate = TRUE,
  callrate_samples = 0.99,
  callrate_probes = 1,
  norm_background = "oob",
  norm_dye = "RELIC",
  norm_quantile = "quantile1",
  array_name = c("EPIC", "450k"),
  annotation_version = c("ilm10b4.hg19", "ilmn12.hg19"),
  n_cores = 1,
  rgSet = NULL,
  echo = FALSE
)

Arguments

directory	A character. Location of IDAT files, default is the current working directory.
csv_file	A character. Path to the sample sheet (csv files) or name of the sample sheet in directory.
meth_value_type	A character. Indicates whether you prefer m-values ("M") or beta-values ("B"). Default is "B".
filter_beads	A logical. Should the probes with a beadcount less than 3 be removed? Default is TRUE.
bead_cutoff	A numeric. The threshold for beadcount. Default is 0.05.
filter_non_cpg	A logical. Should the non-cg probes be removed?
filter_snps	A logical. Should the probes in which the probed CpG falls near a SNP (according to (Zhou et al., 2016)) be removed? Default is TRUE.
population	A character. Name of the ethnicity population to be used. Default is NULL for none.
filter_multihit	A logical. Should the probes which align to multiple locations (according to Nordlund et al., 2013) be removed? Default is TRUE.
filter_xy	A logical. Should the probes from X and Y chromosomes be removed? Default is TRUE.
detection_pvalues	A numeric. The threshold for the detection pvalues above which, values are considered as missing. Default is 0.01.
filter_callrate	A logical. Should the data be filtered based on call rate metric? Default is TRUE.
callrate_samples	A numeric. The call rate threshold for samples, under which samples are excluded. Default is 0.99.
callrate_probes	A numeric. The call rate threshold for probes, under which probes are excluded. Default is 1.
norm_background	A character. Optional method to estimate background normal distribution parameters. This must be one of "oob", "est" or "neg". Default is "oob".
norm_dye	A character. Dye bias correction, "mean": correction based on averaged red/green ratio; or "RELIC": correction with RELIC method; or "none": no dye bias correction. Default is "RELIC".
norm_quantile	A character. The quantile normalisation to be used. This should be one of "quantile1", "quantile2", or "quantile3". Default is "quantile1".
array_name	A character. Choose microarray type, eiyther "450K" or "EPIC". Default is "EPIC".
annotation_version	A character. Version of the annotation package that should be used. Default is "ilm10b4.hg19" for the "EPIC" array
n_cores	An integer. The number of cores to use, i.e., at most how many child processes will be run simultaneously.
rgSet	A RGChannelSet object.
echo	A logical. Should messages be displayed?

Value

A list.

omicsr/dmapaq documentation built on Oct. 13, 2021, 1:08 p.m.