posToProbeAnno: Function for creating a probeAnno environment

Description

This function allows the user to create a probeAnno environment that holds the mapping between probes on the array and their genomic match position(s). As input, the function takes either a.) one of NimbleGen's POS file or a similar file that holds the mapping of probes to the genome. OR b.) a data.frame holding this information

Usage

posToProbeAnno(pos, chrNameColumn = "CHROMOSOME", probeColumn = "PROBE_ID", chrPositionColumn = "POSITION", lengthColumn = "LENGTH", sep="\t", genome="unknown", microarrayPlatform="unknown", verbose = TRUE, ...)

Arguments

pos

either a file-name that specifies the path to the POS or other mapping file OR a data.frame holding the mapping

chrNameColumn

name of the column in the file or data.frame that holds the chromosome name of the match

probeColumn

name of the column that holds the matching probe's unique identifier

chrPositionColumn

name of the column that holds the match genomic position/coordinate on the chromosome

lengthColumn

name of the column that holds the length of the match position, in case of perfect match should correspond to the sequence length of the probe

sep

string; denotes the seperator between elements in the supplied mappings file pos; passed on to function scan; ignored if pos is not a filename.

genome

string; denotes genome (and assembly) the reporters have been mapped to for this probeAnno object, e.g. "M. musculus (mm9)"

microarrayPlatform

string; denotes the commercial or custom microarray platform/design that holds the reporters whose mapping is stored in this probeAnno object, e.g. "NimbleGen MOD SUZ12"

verbose

logical; should progress be written to STDOUT?

...

further arguments passed on to function scan, which is used for reading in the file pos.

Value

The results is an object of class probeAnno.

Details

The default column names correspond to the column names in a NimbleGen POS file.

For custom mappings, using the tools Exonerate, BLAT or MUMmer, the scripts directory of this package holds Perl scripts to generate such a POS file from the respective output files.

Examples

Run this code

 exPos <- read.delim(file.path(system.file("exData",package="Ringo"),
                     "MOD_2003-12-05_SUZ12_1in2.pos"),
                     header=TRUE,as.is=TRUE)
 str(exPos)
 exProbeAnno <- posToProbeAnno(exPos,
     genome="M. musculus (assembly mm8)",
     microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
 ## is equivalent to 
 exProbeAnno2 <- posToProbeAnno(file.path(
    system.file("exData",package="Ringo"),"MOD_2003-12-05_SUZ12_1in2.pos"),
    genome="M. musculus (assembly mm8)",
    microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
 ls(exProbeAnno)
 chromosomeNames(exProbeAnno2)