lumiR.idat: Read Illumina gene expression iDAT files.
In drmjc/lumidat: Methods for importing Illumina gene expression iDAT files

Description Usage Arguments Details Value Author(s) See Also Examples

This function can decrypt Illumina gene expression iDAT files (aka version 1 iDAT files). It will temporarily create GenomeStudio-compatible output files, and then run lumiR.

  lumiR.idat(files = NULL, path = NULL, zipfile = NULL,
    clmfile = NULL,
    probeID = c("ProbeID", "ArrayAddressID", "Sequence", "NuID"),
    manifestfile = NULL,
    collapseMode = c("none", "max", "median", "mean"),
    backgroundCorrect = FALSE, controls = TRUE,
    detectionTh = 0.01, na.rm = TRUE,
    parseColumnName = FALSE, checkDupId = TRUE, QC = TRUE,
    columnNameGrepPattern = list(exprs = "AVG_SIGNAL", se.exprs = "BEAD_STD", detection = "DETECTION", beadNum = "Avg_NBEADS"),
    verbose = FALSE, memory = "-Xmx1024m", ...)

`controls`	logical: if `TRUE`, the controlData slot will be filled, via `lumi::addControlData2lumi`. We recommend this to be `TRUE`.
`detectionTh`	the p-value threshold of determining detectability of the expression. See more details in `lumiQ`.
`na.rm`	logical: remove `NA`?
`parseColumnName`	logical: parse the column names and retrieve the sample information? (Assume the sample information is separated by “\_” from the column type, eg “5356583020_A_AVG_Signal”.)
`checkDupId`	logical: check duplicated TargetIDs or ProbeIds? The duplicated ones will be averaged.
`QC`	logical: do quality control assessment after reading in the data?
`columnNameGrepPattern`	list of named character(1)'s: the grep patterns used to determine which column name corresponds to which slot. Eg the column named “AVG_SIGNAL” will be put into the `exprs` slot.
`...`	other parameters used by `read.table` function
`files`	A character vector of at least one file name
`path`	The path to the directories where the files are. This defaults to the current working directory.
`zipfile`	the path to a zip file containing idat files. This over-rides the `files` argument.
`clmfile`	`NULL`, or the path to a GenePattern-CLM file [5]. This represents a mechanism for renaming, and reordering the samples in the resulting object. Column 1 is the idat name (not path), Column 2 is the desired sample name, column 3 is the biological class of each sample. The order of the rows specifies the order of the samples in the result.
`probeID`	This controls which value to identify each probe by. Allowable values are “ArrayAddressID”, “ProbeID”, “Sequence”, “NuID”.
`manifestfile`	The full path to the Array manifest file in TXT format. See `list_illumina_manifest_files` and then `download_illumina_manifest_file` to download manifest files directly from Illumina.
`collapseMode`	Collapse probes to genes using the specified mode. Valid values are “none” (the default), “max”, “median” and “mean” (the GenomeStudio default).
`backgroundCorrect`	logical, if TRUE then peform background correction on only the gene-level probes; if FALSE, do no correction.
`verbose`	logical, if `TRUE`, print informative messages
`memory`	The maximum Java memory heapsize. eg: "-Xmx1024m", or "-Xmx4g", which reserves 1GB or 4G of RAM, respectively. default="-Xmx1024m"

See preprocess.illumina.idat for more details on Illumina arrays, manifest files, probeID naming options, collapsing probes to genes, and background correcting. Note that lumi provides lumiB for doing background correction (so we usually set backgroundCorrect=FALSE). Also, we usually prefer to collapse from probes to genes after: normalizing, and filtering on probe quality, and expression level, thus we usually select collapseMode="none".

See lumiR for more details on all parameters from detectionTh onwards.

return a LumiBatch-class object

Mark Cowley, with contributions from Mark Pinese, David Eby.

preprocess.illumina.idat lumiR

# iDAT files+path as input
library(lumi)
path <- system.file("extdata", package="lumidat")
files <- c("5356583020_A_Grn.idat", "5356583020_B_Grn.idat")
manifestfile <- system.file("extdata", "HumanHT-12_V3_0_R1_99999999.txt", package="lumidat")
res <- lumiR.idat(files, path, manifestfile=manifestfile, probeID="ProbeID")
res

# zipfile as input
path <- system.file("extdata", package="lumidat")
files <- c("5356583020_A_Grn.idat", "5356583020_B_Grn.idat")
manifestfile <- system.file("extdata", "HumanHT-12_V3_0_R1_99999999.txt", package="lumidat")
zipfile <- tempfile(fileext=".zip")
zip(zipfile, file.path(path, files), flags="-r9Xq")
res <- lumiR.idat(zipfile=zipfile, manifestfile=manifestfile, probeID="ProbeID", verbose=FALSE)
res

# clm file
clmfile <- system.file("extdata", "5356583020.clm", package="lumidat")
res <- lumiR.idat(zipfile=zipfile, manifestfile=manifestfile, probeID="ProbeID", verbose=FALSE, clmfile=clmfile)
sampleNames(res)
# [1] "A" "B"

## Not run: 
# Get the Human HT12 V4 manifest file:
manifestfile <- download_illumina_manifest_file("HumanHT-12_V4_0_R2_15002873_B", "txt")

## End(Not run)