Description Usage Arguments Details Value Author(s)
View source: R/export.gsea.rnk.R
Export a vector of values as a GSEA pre-ranked list.
1 2 |
values |
a numeric vector |
names |
the names associated with each value. If |
file |
the output file name. No hyphens, or a warning will be issued. |
resort |
logical: re-sort the values such that they are decreasing? see order(, decreasing=TRUE) |
sigfigs |
the number of significant figures, defaults to 4. |
up.class |
The up-regulated genes are up in |
down.class |
The down-regulated genes are down in |
Specifying up-/down-regulated genes. One of the
biggest causes of confusion, especially when revisiting
results generated a long time ago, are my positive genes
up in class A, or class B? If you specify up.class
and down.class
, a header is written into in the rnk file.
The new GseaPreRanked GenePattern module will read that
header & label the geneset reports with these names, rather
than na_pos and na_neg.
<none>, makes a file
Mark Cowley, 2008-09-08
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