| Title: | Annotate microarrays and perform cross-species gene expression analyses using flat file databases |
|---|---|
| Description: | Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). |
| Authors: | Alexandre Kuhn <[email protected]> |
| Maintainer: | Alexandre Kuhn <[email protected]> |
| License: | GPL |
| Version: | 1.81.0 |
| Built: | 2024-12-02 05:59:32 UTC |
| Source: | https://github.com/bioc/annotationTools |
Partial Affymetrix annotation for HG-U133A. Used in the example cross-species analysis presented in the vignette of package annotationTools.
data.frame with 188 rows and 43 columns
Concatenates given elements of a list.
compactList(lst,l)compactList(lst,l)
lst |
list object |
l |
numeric vector specifying the number of list elements to be concatenated sequentially |
By definition, the output list is shorter than the input list.
Function stops if 'sum(l)' does not equal 'lenght(lst)'.
clst |
list of length 'length(l)' where the 'i'-th element has length 'l[i]' and contains concatenated elements of input list 'lst'. |
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##an example list lst<-vector('list',3) lst[[1]]<-c('aaa','bbb') lst[[2]]<-'ccc' lst[[3]]<-'zzz' ##merge first 2 list elements compactList(lst,c(2,1))##an example list lst<-vector('list',3) lst[[1]]<-c('aaa','bbb') lst[[2]]<-'ccc' lst[[3]]<-'zzz' ##merge first 2 list elements compactList(lst,c(2,1))
Shortened gene_orthologs database file.
A short version of 'gene_orthologs' table containing 2 ortholog clusters. Ortholog clusters in 'gene_orthologs' derive from NCBI's Eukaryotic Genome Annotation pipeline (see https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/).
ftp.ncbi.nlm.nih.gov/gene/DATA/gene_orthologs.gz
Takes a vector of identifiers and an annotation table and matches the identifiers in the table to retrieve the corresponding annotation. Only the first occurence of each identifier in the annotation table is considered.
getANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 1, annotationCol = 15, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---", sep = " /// ")getANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 1, annotationCol = 15, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---", sep = " /// ")
identifier |
vector containing identifiers to be annotated. |
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. |
identifierCol |
column in annotation table where the provided identifiers are to be looked up. |
annotationCol |
column in annotation table containing the desired annotation. |
noAnnotationSymbol |
character string to be used in output list 'annotation' if no annotation is found or provided. |
noAnnotationProvidedSymbol |
character string used in annotation table and indicating missing annotation. |
sep |
character string used in annotation table to separate multiple annotation of a single identifier. |
The annotation is returned as elements of list 'annotation'. If a single annotation is given for a particular identifier, the corresponding element of 'annotation' has length 1. If multiple annotation is provided for a single identifier (i.e. character string with 'sep' separating multiple annotations), the mulitple annotation is split and the corresponding vector is returned as an element of list 'annotation'.
annotation |
list of length 'length(identifier)' the 'i'-th element of which contains the annotation for 'identifier[i]'. |
empty |
logical vector of length 'length(identifier)'. 'empty[i]' is TRUE if 'identifier[i]' is empty or NA. |
noentry |
locial vector of length 'length(identifier)'. 'noentry[i]' is TRUE if 'identifier[i]' cannot be found in 'annot[,identifierCol]'. |
noannotation |
locial vector of length 'length(identifier)'. 'noannotation[i]' is TRUE if 'a[i]==noAnnotationProvidedSymbol' is TRUE. |
Use getMULTIANNOTATION if the identifiers occur on more than one line in the annotation table.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##example annotation table annotation<-cbind(gene=c('gene_1a, gene_1b','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2','probe_3','probe_4'),sequence=c('sequence_1','sequence_2a, sequence_2c','sequence_3','')) print(annotation) ##get sequences for probe_2, probe_3, probe_4 and probe_100 myProbes<-c('probe_2','probe_3','probe_4','probe_100',NA) getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ') ##track origin of annotation failure for the last 3 probes getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ',diagnose=TRUE)##example annotation table annotation<-cbind(gene=c('gene_1a, gene_1b','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2','probe_3','probe_4'),sequence=c('sequence_1','sequence_2a, sequence_2c','sequence_3','')) print(annotation) ##get sequences for probe_2, probe_3, probe_4 and probe_100 myProbes<-c('probe_2','probe_3','probe_4','probe_100',NA) getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ') ##track origin of annotation failure for the last 3 probes getANNOTATION(myProbes,annotation,identifierCol=2,annotationCol=3,noAnnotationProvidedSymbol='',sep=', ',diagnose=TRUE)
Takes a vector of probe set identifiers and an annotation table and retrieves the corresponding gene IDs.
getGENEID(ps, annot, diagnose = FALSE, idCol = 19, noIDsymbol = NA, noIDprovidedSymbol = "---", sep = " /// ")getGENEID(ps, annot, diagnose = FALSE, idCol = 19, noIDsymbol = NA, noIDprovidedSymbol = "---", sep = " /// ")
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. |
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.
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. |
getANNOTATION provides a more flexible solution to be used with arbitrary annotation tables.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##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)##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)
Takes a vector of probe set identifiers and an annotation table and retrieves the corresponding GO annotation.
getGENEONTOLOGY(ps, annot, diagnose = FALSE, specifics = 0, GOcol = 31, noGOsymbol = NA, noGOprovidedSymbol = "---", sep = " /// ")getGENEONTOLOGY(ps, annot, diagnose = FALSE, specifics = 0, GOcol = 31, noGOsymbol = NA, noGOprovidedSymbol = "---", sep = " /// ")
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. |
specifics |
can take value 0, 1, 2, 3, ... . If specifics=i with i>0, the GO biological process annotation is parsed (using " // " as separator) and the i-th part of the expression is returned. If specifics=0, the GO biological process annotation is not parsed. |
GOcol |
column in annotation table containing the GO biological processes. |
noGOsymbol |
character string to be used in output list 'go' if no GO biological process is found or provided in the annotation table. |
noGOprovidedSymbol |
character string used in annotation table and indicating missing GO biological process. |
sep |
character string used in annotation table to separate multiple GO biological processes. |
This function can be used with Affymetrix annotation files (e.g. 'HG-U133\_Plus\_2\_annot.csv'). It retrieves GO annotation corresponding to particular probe set identifiers. GO biological processes are returned by default ('GOcol'=31) but GO cellular components ('GOcol'=32) or GO molecular functions ('GOcol'=33) can be returned by setting 'GOcol' appropriately.
GO biological processes are returned as elements of list 'go'. If multiple GO biological processes are provided for 'ps[i]' (with 'sep' separating GO biological processes in the annotation table), a vector containing all GO biological processes is returned as the 'i-th' element of list 'go'.
The default values for 'GOcol', 'noGOsymbol', 'noGOprovidedSymbol' 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.
Note that each GO annotation in Affymetrix annotation files contains 3 attributes: the GO biological process ID, term and quality, separated by " // ". Setting the option 'specifics' to 1, 2, or 3 allows to retrieve any of the 3 attributes separately.
go |
list of length 'length(ps)' the 'i'-th element of which contains the GO annotation for 'ps[i]'. |
empty |
logical vector of length 'length(ps)'. 'empty[i]' is TRUE if 'ps[i]' is empty or NA. |
noentry |
locial vector of length 'length(ps)'. 'noentry[i]' is TRUE if 'ps[i]' cannot be found in the first column of the annotation table. |
nogo |
locial vector of length 'length(ps)'. 'nogo[i]' is TRUE if 'go[i]==noIDprovidedSymbol' is TRUE. |
getANNOTATION provides a more flexible solution to be used with arbitrary annotation tables.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##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 GO biological process (full information) myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENEONTOLOGY(myPS,annotation) ##get gene GO biological process terms only getGENEONTOLOGY(myPS,annotation,specifics=2) ##track origin of annotation failure for the 3 last probe set IDs getGENEONTOLOGY(myPS,annotation,diagnose=TRUE) ##GO molecular functions are contained in column 33 of the annotation colnames(annotation) ##get gene GO molecular functions getGENEONTOLOGY(myPS,annotation,GOcol=33)##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 GO biological process (full information) myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENEONTOLOGY(myPS,annotation) ##get gene GO biological process terms only getGENEONTOLOGY(myPS,annotation,specifics=2) ##track origin of annotation failure for the 3 last probe set IDs getGENEONTOLOGY(myPS,annotation,diagnose=TRUE) ##GO molecular functions are contained in column 33 of the annotation colnames(annotation) ##get gene GO molecular functions getGENEONTOLOGY(myPS,annotation,GOcol=33)
Takes a vector of probe set identifiers and an annotation table and retrieves the corresponding gene symbols.
getGENESYMBOL(ps, annot, diagnose = FALSE, GScol = 15, noGSsymbol = NA, noGSprovidedSymbol = "---", sep = " /// ")getGENESYMBOL(ps, annot, diagnose = FALSE, GScol = 15, noGSsymbol = NA, noGSprovidedSymbol = "---", sep = " /// ")
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. |
GScol |
column in annotation table containing the gene IDs. |
noGSsymbol |
character string to be used in output list 'symbols' if no gene symbol is found or provided in the annotation table. |
noGSprovidedSymbol |
character string used in annotation table and indicating missing gene symbol. |
sep |
character string used in annotation table to separate multiple gene symbols. |
This function can be used with Affymetrix annotation files (e.g. 'HG-U133\_Plus\_2\_annot.csv'). It retrieves the gene symbols corresponding to particular probe set identifiers.
Gene symbols are returned as elements of list 'symbols'. If multiple gene symbols are provided for 'ps[i]' (with 'sep' separating gene symbols in the annotation table), a vector containing all gene symbols is returned as the 'i-th' element of list 'symbols'.
The default values for 'GScol', 'noGSsymbol', 'noGSprovidedSymbol' and 'sep' are chosen to suit the format of Affymetrix annotation files. However, these options can be set to look up any annotation table, provided the probe set identifiers are in the first column and occur only once.
symbols |
list of length 'length(ps)' the 'i'-th element of which contains the gene symbol for 'ps[i]'. |
empty |
logical vector of length 'length(ps)'. 'empty[i]' is TRUE if 'ps[i]' is empty or NA. |
noentry |
locial vector of length 'length(ps)'. 'noentry[i]' is TRUE if 'ps[i]' cannot be found in the first column of the annotation table. |
nogs |
locial vector of length 'length(ps)'. 'nogs[i]' is TRUE if 'symbols[i]==noIDprovidedSymbol' is TRUE. |
getANNOTATION provides a more flexible solution to be used with arbitrary annotation tables.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##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 symbols myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENESYMBOL(myPS,annotation) ##track origin of annotation failure for the 3 last probe set IDs getGENESYMBOL(myPS,annotation,diagnose=TRUE)##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 symbols myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENESYMBOL(myPS,annotation) ##track origin of annotation failure for the 3 last probe set IDs getGENESYMBOL(myPS,annotation,diagnose=TRUE)
Takes a vector of probe set identifiers and an annotation table and retrieves the corresponding gene titles.
getGENETITLE(ps, annot, diagnose = FALSE, TITLEcol = 14, noTITLEsymbol = NA, noTITLEprovidedSymbol = "---", sep = " /// ")getGENETITLE(ps, annot, diagnose = FALSE, TITLEcol = 14, noTITLEsymbol = NA, noTITLEprovidedSymbol = "---", sep = " /// ")
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. |
TITLEcol |
column in annotation table containing the gene titles. |
noTITLEsymbol |
character string to be used in output list 'genetitle' if no gene title is found or provided in the annotation table. |
noTITLEprovidedSymbol |
character string used in annotation table and indicating missing gene title. |
sep |
character string used in annotation table to separate multiple gene titles. |
This function can be used with Affymetrix annotation files (e.g. 'HG-U133\_Plus\_2\_annot.csv'). It retrieves the gene titles corresponding to particular probe set identifiers.
Gene titles are returned as elements of list 'genetitle'. If multiple gene titles are provided for 'ps[i]' (with 'sep' separating gene titles in the annotation table), a vector containing all gene titles is returned as the 'i-th' element of list 'genetitle'.
The default values for 'TITLEcol', 'noTITLEsymbol', 'noTITLEprovidedSymbol' and 'sep' are chosen to suit the format of Affymetrix annotation files. However, these options can be set to look up any annotation table, provided the probe set identifiers are in the first column and occur only once.
genetitle |
list of length 'length(ps)' the 'i'-th element of which contains the gene title for 'ps[i]'. |
empty |
logical vector of length 'length(ps)'. 'empty[i]' is TRUE if 'ps[i]' is empty or NA. |
noentry |
locial vector of length 'length(ps)'. 'noentry[i]' is TRUE if 'ps[i]' cannot be found in the first column of the annotation table. |
notitle |
locial vector of length 'length(ps)'. 'noid[i]' is TRUE if 'genetitle[i]==noTITLEprovidedSymbol' is TRUE. |
getANNOTATION provides a more flexible solution to be used with arbitrary annotation tables.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##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 titles myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENETITLE(myPS,annotation) ##track origin of annotation failure for the 3 last probe set IDs getGENETITLE(myPS,annotation,diagnose=TRUE)##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 titles myPS<-c('117_at','1007_s_at','1552288_at',NA,'xyz_at') getGENETITLE(myPS,annotation) ##track origin of annotation failure for the 3 last probe set IDs getGENETITLE(myPS,annotation,diagnose=TRUE)
Takes a vector of gene IDs, a table of homologs/orthologs, and a target species and returns gene IDs corresponding to homologous/orthologous genes.
getHOMOLOG(geneid, targetspecies, homol, cluster = FALSE, diagnose = FALSE, noIDsymbol = NA, clusterCol = 1, speciesCol = 2, idCol = 3, tableType = "homologene")getHOMOLOG(geneid, targetspecies, homol, cluster = FALSE, diagnose = FALSE, noIDsymbol = NA, clusterCol = 1, speciesCol = 2, idCol = 3, tableType = "homologene")
geneid |
character vector containing gene IDs. |
targetspecies |
identifier of the target species in the homology/orthology table. |
homol |
homology/orthology table (data frame) listing gene IDs (1 per line) along with the species and the homology/orthology cluster they belong to. |
cluster |
logical. If TRUE, the identifiers provided in 'geneid' are homology/orthology cluster IDs. If FALSE, they are gene IDs. |
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. |
noIDsymbol |
character string to be used in output list 'targetid' if no homologous/orthologous gene is found or provided in the annotation table. |
clusterCol |
column in homology/orthology table containing homology/orthology cluster IDs. |
speciesCol |
column in homology/orthology table containing species IDs. |
idCol |
column in homology/orthology table containing gene IDs. |
tableType |
character string specifying the type of homology/orthology table used. Either 'homologene' (default) or 'gene_orthologs'. |
The homology/orthology table lists gene IDs (from several species) and the homology/orthology cluster they belong to. Homologous and orthologous genes share a common cluster identifier. Given a certain gene ID, a target species, and a homology/orthology table, all gene IDs belonging to the same homology/orthology cluster and to the specified target species are returned. Various homology/orthology databases can be used, in particular NCBI's HomoloGene and their 'Orthologs from Annotation pipeline', referred to as 'gene_orthologs' database (see details below). If 'targetspecies' is the species 'geneid' belongs to, by definition, homologous genes are returned (if listed). On the contrary, specifying a 'targetspecies' different from the host species 'geneid' belongs to, results in orthologous genes to be returned. Note that each gene ID is assumed to be unique and to belong to a single homology/orthology cluster.
Gene IDs of homologous/orthologous genes are returned as elements of list 'targetid'. If multiple (homologous/orthologous) gene IDs are provided for 'geneid[i]', a vector containing all gene IDs is returned as the 'i-th' element of list 'targetid'.
Default values for 'clusterCol', 'speciesCol', and 'idCol' are chosen to match the table provided by HomoloGene (homologene.data provided by www.ncbi.nlm.nih.gov/HomoloGene). Homology/orthology tables from other sources might require setting these values appropriately.
Orthologs defined in NCBI's 'Orthologs from Annotation pipeline' database (available at ftp.ncbi.nlm.nih.gov/gene/DATA/gene_orthologs.gz, and hence referred to as 'gene_orthologs') can be mined by setting 'tableType' to 'gene_orthologs' instead of 'homologene' (default). In this case, arguments 'clusterCol', 'speciesCol',and 'idCol' are overridden to fit the data structure used in 'gene_orthologs'. In short, one difference between 'gene_orthologs' compared to HomoloGene is that 'gene_orthologs' does not use ortholog cluster IDs but anchors each ortholog groups using the human gene ID of the ortholog group. If a specific ortholog group does not contain a human gene, a gene ID from another species within the ortholog group may be used as anchor.
'gene_orthologs' is a rich source of homologs/orthologs between selected vertebrate species and introduced by NCBI in 2014 (https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/). Note that 'gene_orthologs' does not list (and thus cannot be used to search for) homologs (i.e. only 'Ortholog' relationships, as specified in the 3rd column of 'gene_orthologs' are considered).
Finally, if 'cluster' is TRUE, cluster IDs can be provided in 'geneid' (instead of gene IDs) and the function will return all (homologous/orthologous) gene IDs belonging to a given cluster ID and a given 'targetspecies'. This can be used to mine orthology tables provided by Affymetrix (e.g. 'Mouse430\_2\_ortholog.csv') for orthologous probe set IDs (see 'examples' below).
targetid |
list of length 'length(geneid)' the 'i'-th element of which contains the homologous/orthologous gene IDs for 'geneid[i]' and 'targetspecies'. |
empty |
logical vector of length 'length(geneid)'. 'empty[i]' is TRUE if 'geneid[i]' is empty or NA. |
noentry |
locial vector of length 'length(geneid)'. 'noentry[i]' is TRUE if 'geneid[i]' cannot be found in column 'idCol' (default is column 3) of the homology/orthology table 'homol'. |
notargetid |
locial vector of length 'length(geneid)'. 'notargetid[i]' is TRUE if 'geneed[i]' is found in the homology/orthology table but no homolog/ortholog is listed for 'targetspecies'. |
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##example Homologene file and its location homologeneFile<-system.file('extdata','homologene_part.data',package='annotationTools') ##load Homologene file homologene<-read.delim(homologeneFile,header=FALSE) ##get mouse (species ID 10090) orthologs of several human (species ID 9606) gene ID (among those: 5982, gene symbol RFC2 and 93587, gene symbol: RG9MTD2) myGenes<-c(5982,93587,NA,100) getHOMOLOG(myGenes,10090,homologene) ##track origin of annotation failure for the last 2 gene IDs getHOMOLOG(myGenes,10090,homologene,diagnose=TRUE) ##get mouse gene belonging to homologene cluster IDs 6885 and 6886 myClusters<-c(6885,6886) getHOMOLOG(myClusters,10090,homologene,cluster=TRUE) ##get mouse orthologs of human genes using 'gene_orthologs' gene_orthologsFile<-system.file('extdata','gene_orthologs_part.data',package='annotationTools') gene_orthologs<-read.delim(gene_orthologsFile,header=TRUE) getHOMOLOG(myGenes,10090,gene_orthologs,tableType='gene_orthologs') ##mine Affymetrix (example) ortholog file affyOrthologFile<-system.file('extdata','HG-U133_Plus_2_ortholog_part.csv',package='annotationTools') affyOrthologs<-read.csv(affyOrthologFile,colClasses='character') ##get Mouse430_2 probe set IDs 'orthologous' to HG-U133_Plus_2 probe set IDs 1053_at and 121_at myPS<-c('1053_at','121_at') getHOMOLOG(myPS,'Mouse430_2',affyOrthologs,cluster=TRUE,clusterCol=1,speciesCol=4,idCol=3)##example Homologene file and its location homologeneFile<-system.file('extdata','homologene_part.data',package='annotationTools') ##load Homologene file homologene<-read.delim(homologeneFile,header=FALSE) ##get mouse (species ID 10090) orthologs of several human (species ID 9606) gene ID (among those: 5982, gene symbol RFC2 and 93587, gene symbol: RG9MTD2) myGenes<-c(5982,93587,NA,100) getHOMOLOG(myGenes,10090,homologene) ##track origin of annotation failure for the last 2 gene IDs getHOMOLOG(myGenes,10090,homologene,diagnose=TRUE) ##get mouse gene belonging to homologene cluster IDs 6885 and 6886 myClusters<-c(6885,6886) getHOMOLOG(myClusters,10090,homologene,cluster=TRUE) ##get mouse orthologs of human genes using 'gene_orthologs' gene_orthologsFile<-system.file('extdata','gene_orthologs_part.data',package='annotationTools') gene_orthologs<-read.delim(gene_orthologsFile,header=TRUE) getHOMOLOG(myGenes,10090,gene_orthologs,tableType='gene_orthologs') ##mine Affymetrix (example) ortholog file affyOrthologFile<-system.file('extdata','HG-U133_Plus_2_ortholog_part.csv',package='annotationTools') affyOrthologs<-read.csv(affyOrthologFile,colClasses='character') ##get Mouse430_2 probe set IDs 'orthologous' to HG-U133_Plus_2 probe set IDs 1053_at and 121_at myPS<-c('1053_at','121_at') getHOMOLOG(myPS,'Mouse430_2',affyOrthologs,cluster=TRUE,clusterCol=1,speciesCol=4,idCol=3)
Takes a vector of identifiers and an annotation table and matches the identifiers in the table to retrieve the corresponding annotation. Identifiers can occur on multiple records (i.e. lines) of the annotation table.
getMULTIANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 19, annotationCol = 1, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---")getMULTIANNOTATION(identifier, annot, diagnose = FALSE, identifierCol = 19, annotationCol = 1, noAnnotationSymbol = NA, noAnnotationProvidedSymbol = "---")
identifier |
vector containing identifiers to be annotated. |
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. |
identifierCol |
column in annotation table where the provided identifiers are to be looked up. |
annotationCol |
column in annotation table containing the desired annotation. |
noAnnotationSymbol |
chacter string to be used in output list 'annotation' if no annotation is found or provided. |
noAnnotationProvidedSymbol |
character string used in annotation table and indicating missing annotation. |
The annotation is returned as elements of list 'annotation'. If the 'i'-th identifier occur on multiple lines, all corresponding annotation are retrieved and output as a vector. The length of the 'i'-th element of 'annotation' thus equals the number of lines for 'identifier[i]' in the annotation table.
annotation |
list of length 'length(identifier)' the 'i'-th element of which contains the annotation for 'identifier[i]'. |
empty |
logical vector of length 'length(identifier)'. 'empty[i]' is TRUE if 'identifier[i]' is empty or NA. |
noentry |
locial vector of length 'length(identifier)'. 'noentry[i]' is TRUE if 'identifier[i]' cannot be found in 'annot[,identifierCol]'. |
noannotation |
locial vector of length 'length(identifier)'. 'noannotation[i]' is TRUE if 'a[i]==noAnnotationProvidedSymbol' is TRUE. |
getANNOTATION runs faster and is to be used if the identifiers occur only once in the annotation table.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##example annotation table annotation<-cbind(gene=c('gene_1','gene_2','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2a','probe_2b','','probe_4'),sequence=c('sequence_1','sequence_2a','sequence_2b','','sequence_4')) print(annotation) ##get sequences for gene_2, gene_3, gene_4 and gene_100 myGenes<-c('gene_2','gene_3','gene_4','gene_100', NA) getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='') ##track origin of annotation failure for the 3 last genes getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='',diagnose=TRUE)##example annotation table annotation<-cbind(gene=c('gene_1','gene_2','gene_2','gene_3','gene_4'),probe=c('probe_1','probe_2a','probe_2b','','probe_4'),sequence=c('sequence_1','sequence_2a','sequence_2b','','sequence_4')) print(annotation) ##get sequences for gene_2, gene_3, gene_4 and gene_100 myGenes<-c('gene_2','gene_3','gene_4','gene_100', NA) getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='') ##track origin of annotation failure for the 3 last genes getMULTIANNOTATION(myGenes,annotation,identifierCol=1,annotationCol=2,noAnnotationProvidedSymbol='',diagnose=TRUE)
Used for cross-species analysis of gene expression profiles. Takes a vector of probe sets (species 1), a data.frame containing a second set of probe sets (species 2) and associated values (e.g. log fold change, t-statistic, ...) , a mapping table of orthologous probe sets (species 1 to species 2) and returns the list of probe sets orthologous to those in the first vector and found in the second set.
getOrthologousProbesets(ps1,ps2,ps2ps,fct=function(x){x},forceProbesetSelection=FALSE)getOrthologousProbesets(ps1,ps2,ps2ps,fct=function(x){x},forceProbesetSelection=FALSE)
ps1 |
A vector of probe sets identifiers. |
ps2 |
A data.frame where the first column contains the target probe sets. The second column contains quantities associated with each probe set like e.g. log fold change, t-statistic, etc. |
ps2ps |
A data.frame containing a mapping table of orthologous probe sets. Can be generated with the function ps2ps.R. |
fct |
A function for probe sets selection. The function is applied to the values (second column of ps2) associated with all orthologous probe sets corresponding to a given probe set in ps1. |
forceProbesetSelection |
Logical. If FALSE (default), all orthologous probe sets found in ps2 are returned. If TRUE, only the probe sets associated with values selected with the function fct are returned. |
Each probe set in the first input vector (ps1) is looked up in the mapping table (ps2ps). Orthologous probe sets given in the mapping table and present in the second input argument (more precisely in the first column of ps2) are returned as a list (ps2\_probeSel). By default, values associated with these orthologous probe sets (and given in the second column of ps2) are returned as a list too (ps2\_value).
A function can be specified and applied to the values associated with the orthologous probe sets. This can for instance be used to assign a summary value associated with a set orthologous probe sets (e.g. fct=mean or fct=median in case the associated values are log fold changes). Alternatively, this can be used to filter a single probe set out of multiple orthologous probe sets (e.g. fct=min in case the associated value is a p-value) (see below).
By default, the function returns all orthologous probe sets found. You can force the function to return only the probe sets associated with the values selected by the application of the user-specified function (specify forceProbesetSelection=TRUE). For instance, if the values in the second column of ps2 are p-values and fct=min, for each probe set in ps1 the minimal p-value associated with orthologous probe sets in ps2 is returned (ps2\_value) as well as the probe set associated with the minimal p-value (ps2\_probeSel).
ps2\_probeSel |
A list of orthologous probe sets given by the mapping table (ps2ps) and present in ps2. By default, all orthologous probe sets are returned. If forceProbesetSelection=TRUE, only the probe sets whose values are matched after application of the user-defined function (fct) are returned. |
ps2\_value |
A list of values associated with the orthologous probe sets. By default, all values are returned. If a function is specified (fct), it is applied to the values before they are returned. |
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
data(orthologs_example) ##select the first 3 probe sets listed in 'table_mouse' and their orthologs in 'table_human' ##note that no ortholog is found for the top mouse probe set table_mouse[1:3,] orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human,ortho) orthops[[1]] ##the second item returned contains the values associated with orthologs (second column of 'table_human') orthops[[2]] ##calculates, for each mouse probe set, the median orthologous log fold change (in case of multiple orthologs) ##(in this case log fold changes need to be in the second column of 'table_mouse') orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human,ortho,'median') orthops[[2]] ##for each mouse probe set having multiple orthologous human probe sets ##select the orthologous probe set with the smallest p-value (column 4 of 'table_human') orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human[,c(1,4)],ortho,'min',forceProbesetSelection=TRUE) orthops[[1]] ##orthologous probe set selection can based on arbitrary functions ##e.g. select the 2 orthologous probe sets with the smallest p-values orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human[,c(1,4)],ortho,function(x){sort(x)[1:2]},forceProbesetSelection=TRUE) orthops[[1]]data(orthologs_example) ##select the first 3 probe sets listed in 'table_mouse' and their orthologs in 'table_human' ##note that no ortholog is found for the top mouse probe set table_mouse[1:3,] orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human,ortho) orthops[[1]] ##the second item returned contains the values associated with orthologs (second column of 'table_human') orthops[[2]] ##calculates, for each mouse probe set, the median orthologous log fold change (in case of multiple orthologs) ##(in this case log fold changes need to be in the second column of 'table_mouse') orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human,ortho,'median') orthops[[2]] ##for each mouse probe set having multiple orthologous human probe sets ##select the orthologous probe set with the smallest p-value (column 4 of 'table_human') orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human[,c(1,4)],ortho,'min',forceProbesetSelection=TRUE) orthops[[1]] ##orthologous probe set selection can based on arbitrary functions ##e.g. select the 2 orthologous probe sets with the smallest p-values orthops<-getOrthologousProbesets(table_mouse[1:3,1],table_human[,c(1,4)],ortho,function(x){sort(x)[1:2]},forceProbesetSelection=TRUE) orthops[[1]]
Takes a vector of gene IDs (or identifiers of other types) and an annotation table and looks up the gene IDs in the table to retrieve the corresponding probe set identifiers. Each gene ID can occur multiple times (i.e. on mulitple lines) in the annotation table.
getPROBESET(geneid, annot, uniqueID = FALSE, diagnose = FALSE, idCol = 19, noPSsymbol = NA, noPSprovidedSymbol = "---")getPROBESET(geneid, annot, uniqueID = FALSE, diagnose = FALSE, idCol = 19, noPSsymbol = NA, noPSprovidedSymbol = "---")
geneid |
character vector containing the gene IDs. |
annot |
annotation table (data frame) where each row is a record and each column is an annotation field. |
uniqueID |
logical. If TRUE, only probe set IDs annotated with a single gene ID are returned. If FALSE, probe set IDs annotated with multiple gene IDs are returned too. |
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 identifiers. |
noPSsymbol |
character string to be used in output list 'ps' if no probe set ID is found or provided in the annotation table. |
noPSprovidedSymbol |
character string used in annotation table and indicating missing probe set ID. |
This function can be used with Affymetrix annotation files (e.g. 'HG-U133\_Plus\_2\_annot.csv'). It retrieves probe set IDs corresponding to particular gene identifiers. By default, the function takes gene IDs but any type of identifier (e.g. gene symbol) can be used (set 'idCol' accordingly).
Probe set IDs are returned as elements of list 'ps'. If multiple probe set IDs are found for 'geneid[i]', a vector containing all probe set IDs is returned as the 'i-th' element of list 'ps'.
The default values for 'idCol', 'noPSsymbol', and 'noPSprovidedSymbol' 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.
ps |
list of length 'length(geneid)' the 'i'-th element of which contains the probe set IDs for 'geneid[i]'. |
empty |
logical vector of length 'length(geneid)'. 'empty[i]' is TRUE if 'geneid[i]' is empty or NA. |
noentry |
locial vector of length 'length(geneid)'. 'noentry[i]' is TRUE if 'geneid[i]' cannot be found in column 'idCol' (default is column 19) of the annotation table. |
noid |
locial vector of length 'length(geneid)'. 'noid[i]' is TRUE if 'ps[i]==noIDprovidedSymbol' is TRUE. |
getMULTIANNOTATION provides a more flexible solution that can be used with arbitrary annotation tables.
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##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='#') ##genes of interest myGenes<-c('DDR1','GUCA1A','HSPA6',NA,'XYZ') ##column 15 in annotation contains gene symbols colnames(annotation) ##find probe sets probing for particular genes getPROBESET(myGenes,annotation,idCol=15) ##find probe sets probing only for the genes of interest (i.e. with unique annotation) getPROBESET(myGenes,annotation,idCol=15,uniqueID=TRUE) ##track origin of annotation failure for the 2 last probe set IDs getPROBESET(myGenes,annotation,idCol=15,diagnose=TRUE)##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='#') ##genes of interest myGenes<-c('DDR1','GUCA1A','HSPA6',NA,'XYZ') ##column 15 in annotation contains gene symbols colnames(annotation) ##find probe sets probing for particular genes getPROBESET(myGenes,annotation,idCol=15) ##find probe sets probing only for the genes of interest (i.e. with unique annotation) getPROBESET(myGenes,annotation,idCol=15,uniqueID=TRUE) ##track origin of annotation failure for the 2 last probe set IDs getPROBESET(myGenes,annotation,idCol=15,diagnose=TRUE)
Truncated Affymetrix annotation file for GeneChip array HG-U133 Plus 2.
A table containing 7 probe set IDs and the associated annotation.
Truncated Affymetrix ortholog file for GeneChip array HG-U133 Plus 2.
A table containing 5 probe set IDs and their orthologs probe set IDs on other GeneChip arrays.
Truncated HomoloGene database file.
A table containing 3 homology clusters defined by HomoloGene.
http://www.ncbi.nlm.nih.gov/HomoloGene
Takes a list and returns a character vector by (separately) concatenating the vectors in the list.
listToCharacterVector(lst,sep=' /// ')listToCharacterVector(lst,sep=' /// ')
lst |
list object |
sep |
character string specifying the separator to concatenate each elements of vectors in the list |
The output vector has same length as the input list.
v |
vector of length 'length(lst)' where the 'i'-th element contains the concatenation of the 'i'-th element of 'lst'. |
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
##an example list lst<-vector('list',3) lst[[1]]<-c('a1','a2') lst[[2]]<-'b' lst[[3]]<-c('c1','c2','c3') ##merge first 2 list elements listToCharacterVector(lst,sep=', ')##an example list lst<-vector('list',3) lst[[1]]<-c('a1','a2') lst[[2]]<-'b' lst[[3]]<-c('c1','c2','c3') ##merge first 2 list elements listToCharacterVector(lst,sep=', ')
Truncated Affymetrix annotation file for GeneChip array Mouse 430 2.
A table containing 9 probe set IDs and the associated annotation.
Partial ortholog probe sets mapping table of MG-U74Av2 probe sets to HG-U133A probe sets. Generated with ps2ps.R and Affymetrix annotations for MG-U74Av2 and HG-U133A arrays. Used in the example cross-species analysis presented in the vignette of package annotationTools.
data.frame with 100 rows and 4 columns.
http://www.affymetrix.com for Affymetrix annotations
Takes two Affymetrix annotation files, a table of orthologs (either 'gene_orthologs' or the HomoloGene database), a target species ID and returns a mapping table with homologous/orthologous probe sets.
ps2ps(annotation_1,annotation_2,ortholog,target_species,probesets=NULL,tableType="homologene")ps2ps(annotation_1,annotation_2,ortholog,target_species,probesets=NULL,tableType="homologene")
annotation_1 |
A data.frame with Affymetrix annotation for the source microarray format. |
annotation_2 |
A data.frame with Affymetrix annotation for the target microarray format. |
ortholog |
A data.frame with the HomoloGene or 'gene_orthologs' database. |
target_species |
The target species identifier (i.e. the species corresponding to the target microarray). |
probesets |
A vector of probe set identifiers. If not specified, all probe sets on the source microarray format are mapped (default). |
tableType |
Character string (either 'homologene' or 'gene_orthologs') specifying the type of ortholog table used ('homologene' is the default). |
A table of orthologous/homologous probe sets is built by looking up gene IDs (corresponding to the probe sets on the source microarray array) in HomoloGene or 'gene_orthologs' to find their orthologs, and identifying probe sets in the target microarray that probe the orthologous gene transcripts.
Affymetrix annotation files can be obtained from Affymetrix (http://www.affymetrix.com). A flat file database version can be obtained from HomoloGene (http://www.ncbi.nlm.nih.gov/HomoloGene) or from NCBI's 'Orthologs from Annotation pipeline' database, referred to as 'gene_orthologs' (ftp.ncbi.nlm.nih.gov/gene/DATA/gene_orthologs.gz). Target species ID are defined by the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy)
mappingTable |
A data.frame with four columns and as many rows as there are probe sets in the source annotation. Eache row corresponds to a probe set in the source annotation (column1), the corresponding gene IDs (column 2), the orthologous gene IDs in the target species (column 3), and the probe sets in the target annotation correspondin to the orthologous gene IDs (column 4). |
Alexandre Kuhn
Kuhn et al. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics, 9:26 (2008)
## Not run: ##load Affymetrix annotations annotMouse<-read.csv('Mouse430_2_annot.csv',colClasses='character',comment.char='#') annotHuman<-read.csv('HG-U133A_annot.csv',colClasses='character',comment.char='#') ##load HomoloGene database homologene<-read.delim('homologene.data',header=FALSE) ##define target species ID homoSapiens_ID<-9609 ##map all probe sets on mouse array Mouse 430 2.0 to their orthologs on human array HG-U133A mappingTable<-ps2ps(annotMouse,annotHuman,homologene,homoSapiens_ID) ##write mapping table to disk write.table(mappingTable,file='Mouse4302_HGU133A.txt',sep='\t',col.names=T,row.names=F,quote=FALSE) ##to map the first 10 probe sets given in the annotation only mappingTable<-ps2ps(annotMouse,annotHuman,homologene,targetSpecies,probesets=annotMouse[1:10,1]) ## End(Not run)## Not run: ##load Affymetrix annotations annotMouse<-read.csv('Mouse430_2_annot.csv',colClasses='character',comment.char='#') annotHuman<-read.csv('HG-U133A_annot.csv',colClasses='character',comment.char='#') ##load HomoloGene database homologene<-read.delim('homologene.data',header=FALSE) ##define target species ID homoSapiens_ID<-9609 ##map all probe sets on mouse array Mouse 430 2.0 to their orthologs on human array HG-U133A mappingTable<-ps2ps(annotMouse,annotHuman,homologene,homoSapiens_ID) ##write mapping table to disk write.table(mappingTable,file='Mouse4302_HGU133A.txt',sep='\t',col.names=T,row.names=F,quote=FALSE) ##to map the first 10 probe sets given in the annotation only mappingTable<-ps2ps(annotMouse,annotHuman,homologene,targetSpecies,probesets=annotMouse[1:10,1]) ## End(Not run)
Partial list of probe sets from differential expression analysis of Huntington's disease patients versus controls. Used in the example cross-species analysis presented in the vignette of package annotationTools.
data.frame with 188 rows (probe sets) and 12 columns.
http://hdbase.org/cgi-bin/welcome.cgi
Top 100 probe sets from the differential expression analysis of CHL2 mice versus wild-type mice (MG-U74Av2). Used in the example cross-species analysis presented in the vignette of package annotationTools.
data.frame with 100 rows and 8 columns
http://hdbase.org/cgi-bin/welcome.cgi