IlluminaIdatFiles.jl

Read Illumina idat files
Author oheil
Popularity
0 Stars
Updated Last
1 Year Ago
Started In
November 2020

IlluminaIdatFiles

This is a low level IO package for Illumina .idat files

References

The implementation follows the code of the R bioconductor package illuminaio by

  • Smith, L M, Baggerly, A K, Bengtsson, Henrik, Ritchie, E M, Hansen, D K (2013). “illuminaio: An open source IDAT parsing tool for Illumina microarrays.” F1000Research, 2(264). doi: 10.12688/f1000research.2-264.v1.

Currently supported files

This package is in an early stage and the following microarrays .idat files are supported:

  • Illumina HumanRef-8 Expression BeadChips
  • Illumina HumanHT 12 Gene Expression BeadChip
  • Illumina Infinium MethylationEPIC BeadChip
  • Illumina Infinium Human Methylation 450K BeadChip
  • Illumina Infinium Mouse Methylation BeadChip

e.g. 204792200130_R01C01_Grn.idat, 204792200130_R01C01_Red.idat

Dependencies

Julia versions

  • Julia 1.0 or above

Third party packages

  • LightXML 0.9 (or above but upper bound is mandatory)

Standard Library packages

  • Base64

Usage

General usage

using Pkg
Pkg.add("IlluminaIdatFiles");
#Pkg.add(url="https://github.com/oheil/IlluminaIdatFiles.jl",rev="master")

using IlluminaIdatFiles

To read an illumina idat file use the following command:

idat = idat_read(filename)

Examples:

filename = raw"c:\temp\idat\204792200130_R01C01_Grn.idat"
idat = idat_read(filename)
using GZip
fh = GZip.open("204792200130_R01C01_Red.idat.gz")
idat = idat_read(fh)
close(fh)
using GZip
idat = GZip.open("204792200130_R01C01_Red.idat.gz") |> idat_read
using TranscodingStreams, CodecZlib
stream = GzipDecompressorStream(open("204792200130_R01C01_Red.idat.gz"))
idat = idat_read(stream)
close(stream)
using TranscodingStreams, CodecZlib
idat = GzipDecompressorStream(open("204792200130_R01C01_Red.idat.gz")) |> idat_read

The returned idat is a struct of type IlluminaIdatFiles.Idat:

mutable struct Idat
    nRead::Int32
    data::Dict{String,AbstractArray}
    redGreen::Int32
    mostlyNull::String
    barcode::String
    chipType::String
    mostlyA::String
    unknown1::String
    unknown2::String
    unknown3::String
    unknown4::String
    unknown5::String
    unknown6::String
    unknown7::String
    tenthPercentile::Int
    sampleBeadSet::String
    sentrixFormat::String
    sectionLabel::String
    beadSet::String
    veracodeLotNumber::String
end

Where the most important member is

idat.data

which contains all data (and some other) arrays available in the .idat file:

e.g. Illumina Infinium MethylationEPIC BeadChip:
julia> idat.data
Dict{String,AbstractArray} with 10 entries:
  "IlluminaID"  => [1600101, 1600111, 1600115, 1600123, 1600131,...
  "Mean"        => [3165, 812, 456, 1848, 101, 7450, 5153, 947, 620, 364, ...
  "SD"          => [229, 288, 233, 219, 60, 983, 683, 169,...
  "NBeads"      => [14, 7, 19, 14, 14, 10, 16, 15, 12, 12...
  ...

julia> keys(idat.data)
Base.KeySet for a Dict{String,AbstractArray} with 10 entries. Keys:
  "blockType"
  "NBeads"
  "MidBlock"
  "codeVersion"
  "SD"
  "runTime"
  "blockPars"
  "IlluminaID"
  "Mean"
  "blockCode"
e.g. Illumina HumanHT 12 Gene Expression BeadChip:
julia> idat.data
Dict{String,AbstractArray} with 15 entries:
  "__IllumicodeBinData"    => [10008, 10010, 10014, 10017, 10019, 10020,...
  "__MeanBinData"          => [768.46, 94.0066, 86.5272, 94.533, 112.999,...
  "__NumBeadsBinData"      => [23, 22, 21, 25, 16, 26, 24, 17,...
  ...

julia> keys(idat.data)
Base.KeySet for a Dict{String,AbstractArray} with 15 entries. Keys:
  "__CodesBinData"
  "SoftwareApp"
  "__BackgroundBinData"
  "Date"
  "__IllumicodeBinData"
  "Version"
  "__TrimmedMeanBinData"
  "Name"
  "__BackgroundDevBinData"
  "__DevBinData"
  "__MeanBinData"
  "Parameters"
  "__NumGoodBeadsBinData"
  "__NumBeadsBinData"
  "__MedianBinData"  

The keys are the original data specifiers present in the .idat file, which are different for the different chip types and maybe different between versions.

Used By Packages

No packages found.