racExSet-class {GGtools} | R Documentation |
A container for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
Objects can be created by calls of the form new("racExSet", phenoData, experimentData, annotation, exprs, racs, ...)
.
racAssays
:"AssayData"
SxN matrix
of 0, 1, 2, or NA, rownames are RS numbers from dbSNP, column names
are sampleNames assayData
:"AssayData"
GxN matrix
of expression values rarebase
:SNPalleles
:phenoData
:"AnnotatedDataFrame"
standard
phenoData instance experimentData
:"MIAME"
experiment
level metadata annotation
:"character"
tag .__classVersion__
:"Versions"
R class version
control metadata
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet"
.
Class "Versioned"
, by class "eSet"
.
signature(x = "racExSet")
: accessor for the
racAssay matrix signature(x = "racExSet")
: give RS numbers
for rows of racAssay matrix signature(x = "racExSet")
: accessor for the
racAssays slotsignature(racExSet = "racExSet", geneid = "genesym", snpid = "character", fitfun = "function")
: use a genesym instance (e.g.,
genesym("DDR1")
to identify the expression values,
an rs number to identify the snp genotype information, and
fitfun to fit a model with expression as dependent variable and
genotype (rare allele counts) as predictor. Any fitting
function accepting a formula and data frame should succeed (e.g., lm
). signature(racExSet = "racExSet", geneid = "character", snpid = "character", fitfun = "function")
: as above, but can avoid the lookup of the
gene symbol by supplying the probe set identifier directly. This is
problematic at present as most probe set identifier strings are not
valid R variable names, and so cannot serve directly in the formula.
Some backtick coding is needed to get this to work generally. signature(racExSet = "racExSet", geneid = "list", snpid = "character", fitfun = "function")
: the geneid
parameter must
be a named list of length one with content a numeric vector of
expression values conforming to the snp values. Avoids lookup
of gene name and of expression values.signature(racExSet = "racExSet", geneid = "list" , snpid="formula", fitfun="function")
: the geneid
parameter must be bound to a named list of length 1
with content a numeric vector
with one element per sample; the name of the list element is the gene symbol on
which the numeric vector is a vector of expression values; the
snpid
parameter is bound to a formula template, either
~.
or ~factor(.)
expressing choice between an additive
genetic model and a general model.
Helper functions SNPalleles
and rarebase
are accessors. snps5PrimeTo(gene,rad)
will obtain rs numbers for SNPs in selected locations
relative to the specified gene. snps3PrimeTo
and snpsNear
have similar purposes.
The genesym
class works in conjunction
with annotation to allow translation from HUGO symbols
to affy probe set names according to Bioconductor
annotation environments. The getpsid
function
carries out the translation; the genesym
class/wrapper
just tells us that a string will be serving the role of
a HUGO symbol and allows us to dispatch accordingly. The
snpID
class has similar role. It just lets us
know that a string is intended to be regarded as an rs number.
hgfocusSYMMEMO
is a lookup table quickly establishing
the probeset ID based on a HUGO symbol; likewise mgu74av2SYMMEMO.
chr20GGdem
is a demonstration example of chromosome
20 hapmap snps and hgfocus expression data from GEO as generated by Cheung and colleagues.
gse2031GG
is a demonstration example of BXD mouse
snps and mgu74av2 expression data from GSE2031 in GEO.
The exclMono
function eliminates loci that happen to be monomorphic in the sample.
VJ Carey <stvjc@channing.harvard.edu>
make_racExSet
for construction; eSet
ancestor
class
example(make_racExSet) dem snpNames(dem)[1:4] featureNames(dem)[1:4] oneFit(dem, genesym("DDR1"), "rs4814683", lm) ddr1 = list(DDR1=exprs(dem)["1007_s_at",]) oneFit(dem, ddr1, "rs4814683", aov) data(chr20GGdem) ddr1 = list(DDR1=exprs(chr20GGdem)["1007_s_at",]) summary(oneFit(chr20GGdem, ddr1, ~rs4814683+factor(rs6060535), lm)) dim(snps(chr20GGdem)) dim(snps(exclMono(chr20GGdem)))