posToProbeAnno {Ringo} | R Documentation |
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
posToProbeAnno(pos, chrNameColumn = "CHROMOSOME", probeColumn = "PROBE_ID", chrPositionColumn = "POSITION", lengthColumn = "LENGTH", genome="unknown", microarrayPlatform="unknown", verbose = TRUE, ...)
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 |
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 read.delim
if pos is a file path. |
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.
The results is an object of class probeAnno
.
Joern Toedling toedling@ebi.ac.uk
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)