mbcb.parseFile: MBCB - Model-Based Background Correction for Illumina...

In MBCB: MBCB (Model-based Background Correction for Beadarray)

Description

This function is used to read the files provided into a format which will be usable by the MBCB package (data.frame).

Usage

mbcb.parseFile(sigFile, conFile, isRawBead = FALSE)

Arguments

sigFile	The file-name (character string) representing the signal file.
conFile	The file-name (character string) representing the control file.
isRawBead	A boolean value representing whether the input files are bead-level or bead-type. If the input is bead-level, set this value to True so that the raw bead-level values can be summarized to bead-type data.

Value

This function will return a list containing two data frames: sig and con.

sig:

Represents the signal file.

con:

Represents the negative control data.frame.

Note

The input files should be tab-delimited files in the following form:

signal.txt

				g.1	g.2	g.3	g.4
10181072_239_rc-S	160.3	776.4	135.8	407.7
10181072_290-S		138.1	219.8	122.1	142.4
...			...	...	...	...

neg-con.txt

id	g.1	g.2	g.3	g.4
50133	127	213.5	82	103
50315	232	295	143.5	156
...	...	...	...	...

Note that both of these examples come from a test involving four trials. Your data could use whatever number you'd like.

Author(s)

Yang Xie [e-mail], Min Chen [e-mail], Jeff Allen [e-mail]

See Also

mbcb.correct

Examples

  data(MBCBExpressionData)

  # Create files from the data provided in this package in the current 
  #     directory
  # Obviously, this is the opposite of what the function does, but we need to 
  #     write sample files for the sake of the demonstration
  # The signal and negative control files can be used by calling the above 
  #     command without the writing and reading of the data.
  write.table(expressionSignal, 'signal.txt', sep="\t");
  write.table(negativeControl, 'negative.control.txt', sep="\t");

  #read in those files just created.
  data <- mbcb.parseFile('signal.txt', 'negative.control.txt');
  signal <- data$sig;
  negCon <- data$con;       

MBCB documentation built on Nov. 8, 2020, 5:49 p.m.