isHGNCsymbol: isHGNCsymbol.R
In hyginn/rete: Network Analysis for Cell- and Systems Biology

Description Usage Arguments Details Value Examples

Check whether gene symbols given are valid HGNC gene symbols.

1	isHGNCsymbol(x)

`x`	A character vector

isHGNCsymbol Checks whether the elements of the input vector are valid HGNC gene symbols (case insensitive) by comparing to a subset of existing gene symbols.

The subset of symbols used here contains only approved gene symbols of the following locus types: * gene with protein product * immunoglobulin gene * protocadherin * T-cell receptor gene * RNA: long non-coding, micro, ribosomal, transfer, small nuclear and nucleolar, Y and vault * endogenous retrovirus

This function is a closure that contains the HGNC symbol table in its environment. It is produced as part of the .onLoad() tasks. The supporting table is stored in extdata/HGNCsymbols.RDS. The script that was used to generate this table is in scripts/generateHGNCtable.R.

Checking is done in a case-insensitive manner.

A vector of logicals of length x that contains TRUE for every element that is present in the HGNC symbol table and FALSE for all others.

isHGNCsymbol()                                   # logical()
isHGNCsymbol(NULL)                               # logical()
isHGNCsymbol(0)                                  # FALSE
isHGNCsymbol("A2M")                              # TRUE
isHGNCsymbol(c("123", "234"))                    # vectorized
isHGNCsymbol(c("A1BG", "a1bg", "a1Bg", "A1bG"))  # case insensitive
x <- c(NA, "A1CF", NULL, "a1bg")                 # length preserving:
length(x)                                        #    3
isHGNCsymbol(x)                                  #    FALSE, TRUE, TRUE