| 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\_Set1genome:"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"])