formatGenesExpr(magpie) | R Documentation |
This function creates new data files from existing text file of gene expression profiles to comply to the format required by the class dataset.
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 |
NULL
Write a new file containing the classes label.
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
).
Camille Maumet
## Not run: GeneExprDataFile <- "pathToFile/3genes4samplesTranspose.txt" outGeneExprDataFile <- "pathToFile/3genes4samplesTranspose_formated.txt" formatGenesExpr(GeneExprDataFile, outGeneExprDataFile, transpose=TRUE) ## End(Not run)