getGENEID: Find gene IDs

Description

Takes a vector of probe set identifiers and an annotation table and retrieves the corresponding gene IDs.

Usage

getGENEID(ps, annot, diagnose = FALSE, idCol = 19, noIDsymbol = NA, noIDprovidedSymbol = "---", sep = " /// ")

Arguments

character vector containing the probe sets identifiers.

annot

annotation table (data frame) where each row is a record and each column is an annotation field.

diagnose

logical. If TRUE, 3 (logical) vectors used for diagnostic purpose are returned in addition to the annotation. If FALSE (default) only the annotation is returned.

idCol

column in annotation table containing the gene IDs.

noIDsymbol

character string to be used in output list 'geneid' if no gene ID is found or provided in the annotation table.

noIDprovidedSymbol

character string used in annotation table and indicating missing gene ID.

sep

character string used in annotation table to separate multiple gene IDs.

Value

geneid: list of length 'length(ps)' the 'i'-th element of which contains the gene ID for 'ps[i]'.
empty: logical vector of length 'length(ps)'. 'empty[i]' is TRUE if 'ps[i]' is empty or NA.
noentry: logial vector of length 'length(ps)'. 'noentry[i]' is TRUE if 'ps[i]' cannot be found in the first column of the annotation table.
noid: logial vector of length 'length(ps)'. 'noid[i]' is TRUE if 'geneid[i]==noIDprovidedSymbol' is TRUE.

Details

This function can be used with Affymetrix annotation files (e.g. 'HG-U133\_Plus\_2\_annot.csv'). It retrieves gene IDs corresponding to particular probe set identifiers.

Gene IDs are returned as elements of list 'geneid'. If multiple gene IDs are provided for 'ps[i]' (with 'sep' separating gene IDs in the annotation table), a vector containing all gene IDs is returned as the 'i-th' element of list 'geneid'.

The default values for 'idCol', 'noIDsymbol', 'noIDprovidedSymbol' and 'sep' are chosen to suit the format of Affymetrix annotation files. However, options can be set to look up any annotation table, provided the probe set identifiers are in the first column and occur only once.

Examples

Run this code

##example Affymetrix annotation file and its location
annotationFile<-system.file('extdata','HG-U133_Plus_2_annot_part.csv',package='annotationTools')

##load annotation file
annotation<-read.csv(annotationFile,colClasses='character',comment.char='#')

##get gene IDs
myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at')
getGENEID(myPS,annotation)

##track origin of annotation failure for the 3 last probe set IDs
getGENEID(myPS,annotation,diagnose=TRUE)