Description Usage Arguments Details Value Examples
You can use first example if you already have a phenotype labels file, or use second example if you are interested in gene sets co-expressing with certain gene(s).
1 | make_gsea_input(matrix_file, soft_file, output_dir = ".", gene = NULL)
|
matrix_file |
string. path to GSE series matrix file |
soft_file |
string. path to GSE SOFT file |
output_dir |
string, path to output directory |
gene |
character. HUGO gene symbol(s) of your interested gene(s) |
both NA
and Inf
are not allowed in input files (.txt
& .cls
).
NULL
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
make_gsea_input(
system.file('extdata/GSE51280_series_matrix.txt.gz', package = 'rGEO'),
system.file('extdata/GSE51280_family.soft.gz', package = 'rGEO')
)
make_gsea_input(
system.file('extdata/GSE19161_series_matrix.txt.gz', package = 'rGEO'),
system.file('extdata/GSE19161_family.soft.gz', package = 'rGEO'),
'.', 'EIF4G2'
)
## End(Not run)
|
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