Check whether gene symbols given are valid HGNC gene symbols.
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
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.
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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
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