lumiR {lumi} | R Documentation

## Read in Illumina expression data

### Description

Read in Illumina expression data. We assume the data was saved in a comma or tab separated text file.

### Usage

    lumiR(fileName, sep = NULL, detectionTh = 0.01, na.rm = TRUE, lib = NULL, dec='.', parseColumnName=TRUE,
    columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs='BEAD_STD', detection='Detection', beadNum='Avg_NBEADS'))

### Arguments

`fileName` | fileName of the data file
`sep` | the separation character used in the text file.
`detectionTh` | the p-value threshold of determining detectability of the expression. The detection value less than the detectionTh is claimed as detectable.
`na.rm` | determine whether to remove NA
`lib` | the annotation library used by `addNuId2lumi`
`dec` | the character used in the file for decimal points.
`parseColumnName` | determine whether to parse the column names and retrieve the sample information (assume the naming of the column names are meaningful.)
`columnNameGrepPattern` | the string grep patterns used to determine the slot corresponding columns.

### Details

The function can automatically determine the separation character if it is Tab or comma. Otherwise, the user should specify the separator manually. If the annotation library is provided, the Illumina Id will be replaced with nuID, which is used as the index Id for the lumi annotation packages.

The parameter "columnNameGrepPattern" is designed for some advanced users. It defines the string grep patterns used to determine the slot corresponding columns. For example, for the "exprs" slot in LumiBatch object, it is composed of the columns whose name includes "AVG_SIGNAL". In some cases, the user may not want to read the "detection" and "beadNum" related columns to save memory. The user can set the "detection" and "beadNum" as NA in "columnNameGrepPattern". If the 'se.exprs' is set as NA or the corresponding columns are not available, then lumiR will create a ExpressionSet object instead of LumiBatch object.

Current version of lumiR can adaptively read the output of BeadStudio Verson 1 and 3. The format Version 3 made quite a few changes comparing with previous versions. One change is the detection value. It was called detectable when the detection value is close to one for Version 1 format. However, the detection value became a p-value in the Version 3. As a result, the detectionTh is automatically changed based on the version. The detectionTh 0.01 for the Version 3 will be changed as the detectionTh 0.99 for Version 1. Another big change is that Version 3 separately output the control probe (gene) information and a "Samples Table". As a result, the controlData slot in LumiBatch class was added to keep the control probe (gene) information, and a QC slot to keep the quality control information, including the "Sample Table" output by BeadStudio version 3.

### Value

return a LumiBatch object

### Author(s)

Simon Lin, Pan Du

### See Also

`LumiBatch`, `addNuId2lumi`

### Examples

    ## specify the file name
    # fileName <- 'Barnes_gene_profile.txt' # Not Run
    ## load the data
    # x.lumi <- lumiR(fileName)

    ## load the data with empty detection and beadNum slots
    # x.lumi <- lumiR(fileName, columnNameGrepPattern=list(detection=NA, beadNum=NA))

[Package lumi version 1.4.0 Index]