MAPAmat {Category} | R Documentation |
These functions return a 0/1 incidence matrix with a row for each chromosme band and a column for each gene. Only those chromosome bands with at least one gene annotation will be included.
MAPAmat(chip, univ = NULL, minCount = 0) chrBandInciMat(chip, univ = NULL, minCount = 0) makeChrBandInciMat(chrGraph)
chip |
A string giving the annotation source. For example,
"hgu133plus2" |
univ |
A vector of gene IDs (these should be Entrez IDs for
most annotation sources). The the annotations will be limited to
those in the set specified by univ . If univ is
NULL (default), then the gene IDs are those found in the
annotation data source. |
chrGraph |
A graph object as returned by
makeChrBandGraph |
minCount |
Bands with less than minCount genes will be
excluded from the returned matrix. If minCount is 0 ,
no bands will be removed, this is the default. |
chrBandInciMat
is a DEPRECATED alias for MAPAmat
.
A (0/1) incidence matrix with chromosome bands as rows and gene IDs
as columns. A 1
in m[i, j]
indicates that the
chromosome band rownames(m)[i]
contains the geneID
colnames(m)[j]
.
Seth Falcon
makeChrBandGraph
,
cateGOry
,
probes2MAP
have_hgu95av2.db <- suppressWarnings(require("hgu95av2.db")) if (have_hgu95av2.db) mam <- MAPAmat("hgu95av2.db")