grp2gmt | R Documentation |
GRP files are used by Connectivity Map on-line tool, which stores the
information of a rank-ordered list of probesets. They are simply one-column
text files, each line containing one probeset. grpFiles2gmt
convert
GRP files into GMT-formatted strings, which can be written in GMT files to
be used by GSEA and other tools.
grp2gmt(txt, chiptype, name)
grpFiles2gmt(..., chiptype, n = -1L)
txt |
A vector of character strings, each containing one probeset |
chiptype |
Chip type, normally character representing the microarray
chip type. If the option is missing, or is of value |
name |
Character, name of the gene set (the first field of the GMT file) |
... |
GRP file names |
n |
Integer, number of lines to be read; |
The function grp2gmt
, called by grpFiles2gmt
internally,
annotates probesets when chiptype
is supported by GTI, and transform
them into the GMT format.
If chiptype is provided, the annotate
function is called to
fetch probeset annotations from the databank.
A vector of character strings, each containing one line of a GMT
file. They can be written to a file with the writeLines
function.
It is user's responsibility to check that all GRP files do exist and are readable.
Jitao David Zhang <jitao_david.zhang@roche.com>
See http://www.broadinstitute.org/cmap/index.jsp for the use of GRP files in the Connectivity Map web tool.
up.file <- system.file("extdata/tags_up.grp", package="ribiosExpression")
down.file <- system.file("extdata/tags_down.grp", package="ribiosExpression")
grp2gmt(readLines(up.file, n=-1))
grpFiles2gmt(c(up.file, down.file), n=3)
## Not run:
grp2gmt(readLines(up.file, n=-1), chiptype="HG_U95AV2")
grpFiles2gmt(c(up.file, down.file), n=-1L, chiptype="HG_U95AV2")
## End(Not run)
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