fuseAnnotMatr {wrMisc}

Fuse annotation matrix to initial matrix

Description

In a number of instances experimental measurements and additional information (annotation) are provided by separate objects (matrixes) as they may not be generated the same time. The aim of this function is provide help when matching approprate lines for 2 sets of data (experimental measures in iniTab and annotation from annotTab) for fusing. fuseAnnotMatr adds suppelmental columns/annotation to an initial matrix iniTab : using column 'refIniT' as key (in iniTab) to compare with key 'refAnnotT' (from 'annotTab'). The columns to be added from annotTab must be chosen explicitely. Note: if non-unique IDs in iniTab : runs slow (but save) due to use of loop for each unique ID.

Usage

fuseAnnotMatr(
  iniTab,
  annotTab,
  refIniT = "Uniprot",
  refAnnotT = "combName",
  addCol = c("ensembl_gene_id", "description", "geneName", "combName"),
  debug = TRUE,
  silent = FALSE,
  callFrom = NULL
)

Arguments

iniTab

(matrix), that may have lines with multiple (=repeated) key entries

annotTab

(matrix) containing reference annotation

refIniT

(character) type of reference (eg 'Uniprot')

refAnnotT

(character) column name to use for reference-annotation

addCol

(character) column-namess of 'annotTab' to use/extract (if no matches found, use all)

debug

(logical) for bug-tracking: more/enhanced messages

silent

(logical) suppress messages

callFrom

(character) allow easier tracking of message(s) produced

Value

combined matrix (elements not found in 'annotTab' are displayed as NA)

See Also

merge

Examples

tab0 <- matrix(rep(letters[1:25],8),ncol=10)
tab1 <- cbind(Uniprot=paste(tab0[,1],tab0[,2]),col1=paste(tab0[,3],
  tab0[,4],tab0[,5]," ",tab0[,7],tab0[,6]))
tab2 <- cbind(combName=paste(tab0[,1],tab0[,2]),col2=paste(tab0[,8],tab0[,9],tab0[,10]))
fuseAnnotMatr(tab1,tab2[c(20:11,2:5),],refIni="Uniprot",refAnnotT="combName",addCol="col2")
fuseAnnotMatr(tab2[c(20:11,2:5),],tab1,refAnnotT="Uniprot",refIni="combName",addCol="col1")