Efficiently import idats files mostly using minfi functions.

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)

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.

Value

A list.