Efficiently import idats files mostly using minfi functions.

read_idats(directory = getwd(), csv_file = "csv\$",
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. A character. Path to the sample sheet (csv files) or name of the sample sheet in directory. A character. Indicates whether you prefer m-values ("M") or beta-values ("B"). Default is "B". A logical. Should the probes with a beadcount less than 3 be removed? Default is TRUE. A numeric. The threshold for beadcount. Default is 0.05. A logical. Should the non-cg probes be removed? 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. A character. Name of the ethnicity population to be used. Default is NULL for none. A logical. Should the probes which align to multiple locations (according to Nordlund et al., 2013) be removed? Default is TRUE. A logical. Should the probes from X and Y chromosomes be removed? Default is TRUE. A numeric. The threshold for the detection pvalues above which, values are considered as missing. Default is 0.01. A logical. Should the data be filtered based on call rate metric? Default is TRUE. A numeric. The call rate threshold for samples, under which samples are excluded. Default is 0.99. A numeric. The call rate threshold for probes, under which probes are excluded. Default is 1. A character. Optional method to estimate background normal distribution parameters. This must be one of "oob", "est" or "neg". Default is "oob". 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". A character. The quantile normalisation to be used. This should be one of "quantile1", "quantile2", or "quantile3". Default is "quantile1". A character. Choose microarray type, eiyther "450K" or "EPIC". Default is "EPIC". A character. Version of the annotation package that should be used. Default is "ilm10b4.hg19" for the "EPIC" array An integer. The number of cores to use, i.e., at most how many child processes will be run simultaneously.

## Value

A list.