formatGenesExpr(magpie)R Documentation

formatGenesExpr: Format your class labels data file to be compatible with the class dataset

Description

This function creates new data files from existing text file of gene expression profiles to comply to the format required by the class dataset.

Arguments

geneExprDataFile character. URL of the input file containing the gene expression
outGeneExprDataFile character. URL of the output file containing the gene expression
rowNames logical. Presence (TRUE) or Absence (FALSE) of the gene names (or sample names if transpose=TRUE)
colNames logical. Presence (TRUE) or Absence (FALSE) of the sample names (or gene names if transpose=TRUE)
separator character. The field separator string. Values within each row of geneExprDataFile are separated by this string. (default "" corresponds to any blank character " " "t"...)
transpose logical. TRUE if samples corresponds to rows and genes to columns
normalize logical. TRUE if the values of gene expresion must be normalized
lineNorm logical. Ignored if normalize is FALSE. TRUE if the rows of the gene expression matrix must be normalized
colNorm logical. Ignored if normalize is FALSE. TRUE if the columns of the gene expression matrix must be normalized
firstLineNorm logical. Ignored if normalize or lineNorm or colNorm is FALSE. TRUE if the rows of the gene expression matrix must be normalized before the columns

Value

NULL
Write a new file containing the classes label.

Using this function

formatGenesExpr(geneExprDataFile, outGeneExprDataFile, rowNames = FALSE, colNames = FALSE, separator = "", transpose = FALSE, normalize = FALSE, lineNorm = FALSE, colNorm = FALSE, firstLineNorm = FALSE)

Create a new file outGeneExprDataFile containing the gene expression profile of each sample from the data file geneExprDataFile. If the sample names are not provided they are automatically generated as X1, X2 ... Xn. If the gene names are not provided they are automatically generated as gene01, gene02 ... genen. The separator is the sequence of character that values of gene expression. Usually rows of the input data file corresponds to genes and columns to sample bur if it's not the case, the user should set transpose to TRUE. The data can also be normalized before storage in the new file by setting normalize to true and selecting the corresponding options (lineNorm, colNorm, firstLineNorm).

Author(s)

Camille Maumet

See Also

dataset, formatClasses

Examples

## Not run: 
GeneExprDataFile <- "pathToFile/3genes4samplesTranspose.txt"
outGeneExprDataFile <- "pathToFile/3genes4samplesTranspose_formated.txt"

formatGenesExpr(GeneExprDataFile, outGeneExprDataFile, transpose=TRUE)
## End(Not run)

[Package magpie version 0.1 Index]