getGENEID: Find gene IDs

In alexandremkuhn/annotationTools: Annotate microarrays and perform cross-species gene expression analyses using flat file databases

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

ps	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.

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.

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.

Note

getANNOTATION provides a more flexible solution to be used with arbitrary annotation tables.

Author(s)

Alexandre Kuhn

References

Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)

See Also

getANNOTATION

Examples

##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)

alexandremkuhn/annotationTools documentation built on April 5, 2020, 12:59 a.m.