Description Usage Arguments Details Value Examples
View source: R/utils_Contains.R
Check if any or all of the elements of a short atomic vector are contained within a supplied long atomic vector.
1 |
long |
A vector to possibly containing any or all elements of
|
short |
A short vector or scalar, some elements of which may be
contained in |
matches |
Should partial set matching of |
partial |
Should partial string matching be allowed? Defaults to
|
This is a helper function to find out if a gene symbol or some similar character string (or character vector) is contained in a pathway. Currently, this function uses base R, but we can write it in a compiled language (such as C++) to increase speed later.
For partial matching (partial = TRUE
), long
must be an
atomic vector of type character, short
must be an atomic scalar (a
vector with length of 1) of type character, and matches
should be
set to "any"
. Because this function is designed to match gene
symbols or CpG locations, we care if the symbol or location starts with
the string supplied. For example, if we set short = "PIK"
, then we
want to find if any of the gene symbols in the supplied long
vector belong to the PIK gene family. We don't care if this string appears
elsewhere in a gene symbol.
A logical scalar. If matches = "any"
, this indicates if any
of the elements of short
are contained in long
. If
matches = "all"
, this indicates if all of the elements of
short
are contained in long
. If partial = TRUE
, the
returned logical indicates whether or not any of the character strings in
long
start with the character scalar supplied to
short
.
1 2 3 4 5 6 7 8 9 10 11 | Contains(1:10, 8)
Contains(LETTERS, c("A", "!"), matches = "any")
Contains(LETTERS, c("A", "!"), matches = "all")
genesPI <- c(
"PI4K2A", "PI4K2B", "PI4KA", "PI4KB", "PIK3C2A", "PIK3C2B", "PIK3C2G",
"PIK3C3", "PIK3CA", "PIK3CB", "PIK3CD", "PIK3CG", "PIK3R1", "PIK3R2",
"PIK3R3", "PIK3R4", "PIK3R5", "PIK3R6", "PIKFYVE", "PIP4K2A",
"PIP4K2B", "PIP5K1B", "PIP5K1C", "PITPNB"
)
Contains(genesPI, "PIK3", partial = TRUE)
|
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