posToProbeAnno {Ringo} | R Documentation

## 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`.

### 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.

### Value

The results is an object of class `probeAnno`.

### Author(s)

Joern Toedling

### See Also

`probeAnno-class`, `scan`

### Examples

     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)

[Package Ringo version 1.58.0 Index]