WhichPathways {pathwayPCA} | R Documentation |
pathwayCollection
-class Object by Symbol.The filter-subset method for pathways lists as returned by the
read_gmt
function. This function returns the subset of
pathways which contain the set of symbols requested
WhichPathways(x, symbols_char, ...)
x |
An object of class |
symbols_char |
A character vector or scalar of gene symbols or regions |
... |
Additional arguments passed to the |
This function finds the index of each set that contains the symbols
supplied, then returns those sets as a new pathwayCollection
object. Find pathways that contain geneA OR geneB by passing the argument
matches = "any"
through ...
to Contains
(this
is the default value). Find pathways that contain geneA AND geneB by
changing this argument to matches = "all"
. Find all genes in a
specified family by passing in one value to short
and setting
partial = TRUE
.
An object of class pathwayCollection
, but containing only the
sets which contain the symbols supplied to symbols_char
. If no sets
are found to contain the symbols supplied, this function returns
NULL
and prints a warning.
data("colon_pathwayCollection") WhichPathways(colon_pathwayCollection, "MAP", partial = TRUE) WhichPathways( colon_pathwayCollection, c("MAP4K5", "RELA"), matches = "all" )