ParseMatrixFile: Helper function to read clinical annotation from GEO Matrix...

In sagade/inf460: Misc tools for daily analysis

Description

Helper function to read clinical annotation from GEO Matrix Series files

Usage

ParseMatrixFile(file, start.line, end.line, pattern.search,
  pattern.extract = "^.*:\\s*", drop.first.col = T, ...)

Arguments

file	the name of the matrix series file
start.line	the number of the line holding the names of the samples
end.line	the line after (!) the last line to read
pattern.search	a named character vector giving the search pattern for the different clinical parameters, names should be the names of the pararmeters
pattern.extract	character vector holding the pattern for extraction the desired parameter value, set to "" if no extraction is need, vector is recycled to same length as pattern.search
drop.first.col	boolean, indicates if the first column of the file contains line descriptors and thus should be dropped, default to TRUE
...	further arguments to sub

Value

a data frame with the parameters specified in pattern.search

sagade/inf460 documentation built on Dec. 31, 2020, 3:15 a.m.