Description Usage Arguments Details Value Author(s) See Also Examples
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
1 2 3 4 | posToProbeAnno(pos, chrNameColumn = "CHROMOSOME",
probeColumn = "PROBE_ID", chrPositionColumn = "POSITION",
lengthColumn = "LENGTH", sep="\t", 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
|
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 |
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 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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