unifyMappings {AnnBuilder}R Documentation

A function to unify mapping result from different sources

Description

Given a base file and mappings from different sources, this function resolves the differences among sources in mapping results using a voting sheme and derives unified mapping results for targets in the base file

Usage

unifyMappings(base, ll, ug, otherSrc, fromWeb)

Arguments

base base a matrix with two columns. The first column contains the target items (genes) to be mapped and the second the know mappings of the target to GenBank accession numbers or UniGene ids
ll ll an object of class LL
ug ug an object of class UG
otherSrc otherSrc a vector of character strings for names of files that also contain mappings of the target genes in base. The files are assumed to have two columns with the first one being target genes and second one being the desired mappings
fromWeb fromWeb a boolean to indicate whether the source data will be read from the web or a local file

Details

ll and ug have methods to parse the data from LocusLink and UniGene to obtain desored mappings to target genes in base. Correct source urls and parsers are needed to obtain the desired mappings

Value

The function returns a matrix with four columns. The first two are the same as the columns of base, the third are unified mappings, and forth are statistics of the agreement among sources.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

See Also

LL, UG

Examples

myDir <- file.path(.path.package("AnnBuilder"), "temp")
geneNMap <- matrix(c("32468_f_at", "D90278", "32469_at", "L00693",
                   "32481_at", "AL031663", "33825_at", " X68733",
                   "35730_at", "X03350", "36512_at", "L32179",
                   "38912_at", "D90042", "38936_at", "M16652",
                   "39368_at", "AL031668"), ncol = 2, byrow = TRUE)
colnames(geneNMap) <- c("PROBE", "ACCNUM")
write.table(geneNMap, file = file.path(myDir, "geneNMap"), sep = "\t",
quote = FALSE, row.names = FALSE, col.names = FALSE)

temp <- matrix(c("32468_f_at", NA, "32469_at", "2",
                   "32481_at", NA, "33825_at", " 9",
                   "35730_at", "1576", "36512_at", NA,
                   "38912_at", "10", "38936_at", NA,
                   "39368_at", NA), ncol = 2, byrow = TRUE)
temp
write.table(temp, file = file.path(myDir, "srcone"), sep = "\t",
quote = FALSE, row.names = FALSE, col.names = FALSE)
temp <- matrix(c("32468_f_at", NA, "32469_at", NA,
                   "32481_at", "7051", "33825_at", NA,
                   "35730_at", NA, "36512_at", "1084",
                   "38912_at", NA, "38936_at", NA,
                   "39368_at", "89"), ncol = 2, byrow = TRUE)
temp
write.table(temp, file = file.path(myDir, "srctwo"), sep = "\t",
quote = FALSE, row.names = FALSE, col.names = FALSE)
otherMapping <- c(srcone = file.path(myDir, "srcone"),
srctwo = file.path(myDir, "srctwo"))

baseFile <-  file.path(myDir, "geneNMap")
llParser <- file.path(.path.package("AnnBuilder"), "data", "gbLLParser")
ugParser <- file.path(.path.package("AnnBuilder"), "data", "gbUGParser")
if(.Platform$OS.type == "unix"){
    llUrl <-  "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz"
    ugUrl <-  "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz"
    fromWeb = TRUE
}else{
    llUrl <- file.path(.path.package("AnnBuilder"), "data", "Tll_tmpl")
    ugUrl <- file.path(.path.package("AnnBuilder"), "data", "Ths.data")
    fromWeb = FALSE
}
ll <- LL(srcUrl = llUrl, parser = llParser, baseFile = baseFile)
ug <- UG(srcUrl = ugUrl, parser = ugParser, baseFile = baseFile,
organism = "human") 
# Only works interactively
if(interactive()){
    unified <- unifyMappings(base =  geneNMap, ll = ll, ug = ug,
               otherSrc = otherMapping, fromWeb = fromWeb)
    read.table(unified, sep = "\t", header = FALSE)

    unlink(c(file.path(myDir, "geneNMap"), file.path(myDir, "srcone"),
    file.path(myDir, "srctwo"), unified))
}
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