read_Illu_expr_array: Reading expression data from Illumina arrays

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Create an ExpressionSetIllumina object from Illumina GenomeStudio output files.

Usage

read_Illu_expr_array(
  dataFile,
  qcFile,
  sampleSheet,
  ProbeID = "ProbeID",
  skip = 0,
  controlID = "ProbeID",
  qc.skip = 0,
  qc.columns = list(exprs = "AVG_Signal", Detection = "Detection Pval"),
  sampleColumn = "Sample_Name",
  groupColumn = "Sample_Group",
  exprchip = NULL,
  org = NULL,
  covarfile = NULL,
  covarsampleID = "ID",
  method_norm = "none",
  transform = "log2",
  fields2Add = NULL
)

Arguments

dataFile	character with filepath to SampleProbeProfile from GenomeStudio (tab-delimited txt-file) containing columns with AVG_Signal, Detection Pval, BEAD_STDERR und Avg_NBEADS. Additional columns are ignored except for "PROBE_ID", "SYMBOL" and "ENTREZ_GENE_ID".
qcFile	character with filepath to ControlProbeProfile from GenomeStudio (tab-delimited txt-file) containing columns with AVG_Signal und Detection Pval
sampleSheet	character with filepath to Sample sheet from GenomeStudio project (csv-file). The header is expected in row 8.
ProbeID	character string with name of the column in dataFile that contains identifiers used to uniquely identify each probe
skip	number of header lines to skip at the top of dataFile.
controlID	character string specifying the column in qcFile that contains the identifiers that uniquely identify each control probe. If the ControlGeneProfile from GenomeStudio is used, you will need to set controlID="TargetID"
qc.skip	number of header lines to skip at the top of qcFile
qc.columns	list defining the column headings in qcFile which correspond to the matrices stored in the QCInfo slot of the final ExpressionSetIllumina object
sampleColumn	Name of sample column in sample sheet
groupColumn	Name of group column in sample sheet
exprchip	character string specifying expression chip type (e.g. "HumanHT-12 v4", "MouseWG-6 v2", "MouseRef-8 v2", "RatRef-12 v1".
org	character string specifying organism: "human", "rat", "mouse".
covarfile	character with filepath if a covariates file is given. NULL otherwise.
covarsampleID	character with name of sample column in (optional) covariates file.
method_norm	character with normalisation method. Options are "quantile", "qspline", "vsn", "rankInvariant", "median" and "none"
transform	character with data transformation method. Options are "none", "log2", "neqc", "rsn" and "vst".
fields2Add	character vector with names of Illumina mappings to add to feature data (chip type dedicated in exprchip). Remark: works only if feature data is "PROBE_ID", but this identifier may be non-unique and may therefore throw an error when loading.

Details

Unnormalized expression data from an Illumina GenomeStudio project is read into a ExpressionSetIllumina object. If a covariate file is given, covariates are included into the phenotype data of the object. If a paired sample design was chosen, the variable indicating sample pairing must be included either in the sample sheet file or in the covariates file. In default settings, the expression data is log2-transformed but not normalized. The feature data of the ExpressionSetIllumina object is supplemented by annotation data given in the respective Illumina annotation package (if available REANNOTATED-columns used). The respective chip-type is given in exprchip.

Value

Annotated (and log-transformed) ExpressionSetIllumina object

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.