smlSet-class {GGtools} | R Documentation |
Efficient representation of SNP+expression data, based on Clayton snpMatrix package. Supports efficient subsetting of whole-genome snp genotyping by chromosome.
Objects can be created by calls of the form new("smlSet", smlEnv, assayData, phenoData, featureData, experimentData, annotation, ...)
.
smlEnv
:"environment"
– there is
one key 'smList' with value a list of snp.matrix
from snpMatrix package snpLocPathMaker
:chromInds
:"numeric"
, a numeric
vector telling what chromosomes are represented. If chromosomes 20 and 21
are present, the values is c(20,21). X and Y are 23, 24.organism
:"character"
; string such as Hs for
modern humans. assayData
:"AssayData"
; container for
expression data as in ExpressionSet phenoData
:"AnnotatedDataFrame"
; container
for sample data as in ExpressionSet featureData
:"AnnotatedDataFrame"
; container
for expression feature data as in ExpressionSetexperimentData
:"MIAME"
; container for MIAME
schema annotation
:"character"
; vector with
names exprs
and snps
; exprs
should be the name of a
SQLite-based Bioconductor annotation package .__classVersion__
:"Versions"
~~
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
signature(x = "smlSet")
: subsetting must be done with care.
The usual idiom is X[G, S]
where G
restricts reporters and
S
restricts samples. Reporter restriction:
At present one can use an instance of chrnum
class to obtain
a subsetted object with SNP data restricted to specified chromosomes.
Sample restriction: works in the customary way for eSet
instances. signature(object = "smlSet")
: return the
expression data matrix. signature(sym = "genesym", sms = "smlSet")
: Execute
snpMatrix snp.rhs.tests for all SNP in the genome. Returns instance
of gwSnpScreenResult. signature(sym = "genesym", sms = "smlSet",
cnum="chrnum")
: Execute
snpMatrix snp.rhs.tests for all SNP on the specific
chromosome. Returns instance
of cwSnpScreenResult. signature(x = "smlSet")
: returns number of samples. signature(x = "smlSet", chrind = "numeric")
: returns
byte (raw) representation of SNP data in snp.matrix format for specified
chromosome. signature(x = "smlSet")
: returns
all relevant locations in order of rs numbers in the
snp.matrices as a single vectorsignature(x = "smlSet")
: returns
all relevant chromosome assignments in order of rs numbers in the
snp.matrices as a single vectorsignature(object = "smlSet")
: returns
vector of sample names. signature(object = "smlSet")
: prints short report. signature(x = "smlSet")
: returns the list of
snp.matrix encoding genotypes. signature(x = "smlSet")
: returns the environment
in which the smList list is contained. VJ Carey <stvjc@channing.harvard.edu>
#showClass("smlSet") data(hmceuB36.2021) rawSNP(hmceuB36.2021, 20)[1:5,1:5] exprs(hmceuB36.2021)[1:5,1:5]