snp.matrix-class {snpMatrix} | R Documentation |
This class defines objects holding large arrays of single nucleotide polymorphism (SNP) genotypes generated using array technologies.
Objects can be created by calls of the form new("snp.matrix", x)
where x
is a matrix with storage mode "raw"
.
Chips (usually corresponding to samples or
subjects) define rows of the matrix while polymorphisms (loci) define
columns. Rows and columns will usually have names which can be
used to link the data to further data concerning samples and SNPs
.Data
:"matrix"
and storage
mode raw
Internally, missing data are coded 00 and SNP genotypes are coded
01, 02 or 03.
Class "matrix"
, from data part.
Class "structure"
, by class "matrix"
.
Class "array"
, by class "matrix"
.
Class "vector"
, by class "matrix", with explicit coerce.
Class "vector"
, by class "matrix", with explicit coerce.
signature(x = "snp.matrix")
: subset
operationssignature(x = "snp.matrix", y = "snp.matrix")
:
S4 generic function to provide cbind() for two or
more matrices together by column. Row names must match and column
names must not coincide. If the matrices are of the derived class
X.snp.matrix-class
, the Female
slot values must also
agreesignature(from = "snp.matrix", to = "numeric")
:
map to codes 0, 1, 2, or NAsignature(from = "snp.matrix", to =
"character")
: map to codes "A/A", "A/B", "B/B", ""signature(from = "matrix", to = "snp.matrix")
:
maps numeric matrix (coded 0, 1, 2 or NA) to a snp.matrixsignature(from = "snp.matrix", to =
"X.snp.matrix")
:
maps a snp.matrix to an X.snp.matrix. Sex is inferred from the
genotype data since males should not be heterozygous at any locus.
After inferring sex, heterozygous calls for males are set to
NA
signature(x = "snp.matrix")
: returns a logical
matrix indicating whether each element is NA
signature(x = "snp.matrix", y = "snp.matrix")
:
S4 generic function to provide rbind() for two or
more matrices by row. Column names must match and duplicated row
names prompt warningssignature(object = "snp.matrix")
: shows the size
of the matrix (since most objects will be too large to show in full)signature(object = "snp.matrix")
: calculate
call rates, allele frequencies, genotype frequencies, and z-tests for
Hardy-Weinberg equilibrium. Results are returned as a dataframe with
column names Calls
, Call.rate
, MAF
, P.AA
,
P.AB
, P.BB
, and z.HWE
signature(x = "snp.matrix")
: returns a logical
matrix of missing call indicatorssignature(x = "snp.matrix", snps
="ANY")
: Recode specified columns of of the matrix to reflect
allele switches
This class requires at least version 2.3 of R
David Clayton david.clayton@cimr.cam.ac.uk
http://www-gene.cimr.cam.ac.uk/clayton
snp-class
, X.snp-class
,
X.snp.matrix-class
data(testdata) summary(summary(Autosomes)) # Just making it up - 3-10 will be made into NA during conversion snps.class<-new("snp.matrix", matrix(1:10)) snps.class if(!isS4(snps.class)) stop("constructor is not working") pretend.X <- as(Autosomes, 'X.snp.matrix') if(!isS4(pretend.X)) stop("coersion to derived class is not S4") if(class(pretend.X) != 'X.snp.matrix') stop("coersion to derived class is not working") pretend.A <- as(Xchromosome, 'snp.matrix') if(!isS4(pretend.A)) stop("coersion to base class is not S4") if(class(pretend.A) != 'snp.matrix') stop("coersion to base class is not working")