probeAnno-class {Ringo} | R Documentation |
A class that holds the mapping between reporters/probes on a microarray and their genomic match position(s) in a chosen genome.
Objects can be created by calls of the form new("probeAnno",
map, arrayName, genome)
.
map
:"environment"
This map
consists of four vectors for each chromosome/strand, namely, say
for chromosome 1:
data.frame
. An entry of '0' indicates
that the probe matching at this position has only this one
match.arrayName
:"character"
, the
name or identifier of the microarray design,
e.g. 2005-06-17\_Ren\_MM5Tiling\_Set1
genome
:"character"
, which
genome the reporters have been mapped tomap
environmentmap
environmentmap
environmentmap
environment map
slot
'probeAnno' objects used to be environments and are still in
package tilingArray
Joern Toedling toedling@ebi.ac.uk; Wolfgang Huber
posToProbeAnno
pa <- new("probeAnno") pa["X.start"] <- seq(5000,10000,by=1000) if (interactive()) show(pa) pa2 <- posToProbeAnno(file.path(system.file("exData",package="Ringo"), "MOD_2003-12-05_SUZ12_1in2.pos")) arrayName(pa2) <- "NimbleGen MOD_2003-12-05_SUZ12_1in2" genome(pa2) <- "H. sapiens (hg18)" show(pa2) head(pa2["9.start"])