as.geneSet {GeneticsBase} | R Documentation |
Convert an existing object to a geneSet. Methods currenrly exist only for matrix and data.frame objects.
## S3 method for class 'matrix': as.geneSet(x, ... ) ## S3 method for class 'data.frame': as.geneSet(x, gene.columns, format=c("single", "adjacent"), ploidy=2, alleles=NULL, sep="/", remove.spaces=TRUE, reorder=c("freq", "yes", "no", "default", "ascii"), allow.partial.missing=FALSE, markerNames, phase=list(F), ...)
x |
The matrix or data.frame object to be converted |
gene.columns |
Names or indexes of columns containing genotypes |
format |
One of "single", indiciating that each specified column
contains a complete genotype (e.g. "A/C"), or "adjacent" indicating
that sets of ploidy adjacent columns each contain as single
allele (e.g. "A", "C") |
ploidy |
Number of allele copies per genotype. Defaults to 2 |
alleles |
Not currently supported. In the future, this variable will allow specification of the allele strings for each genotype. |
sep |
A character value or a numeric index vector indicating how
allels are spearated within genotypes, defaults to "/". If a
character, it indicates that alleles within a genotype are
separated by this character (e.g. for "A/C", sep="/" ). If a
numeric vector (of length ploidy -1), the value(s) indicate
which positions separate allele names (e.g. for "AA", sep=1 ).
|
remove.spaces |
Should whitespace be removed before processing. |
reorder |
One of "freq", "yes", "no", "default", or "ascii",
indicating whether and how alleles should be reorderd within
genotypes.
If reorder="no" , the observed order is preserved
(important when phase is known).
If reorder="freq" , sort
alleles within each individual by observed frequency.
If reorder="yes" , sort alleles in the order provided by the
alleles argument.
If reorder="ascii" , reorder alleles in ASCII order
(alphabetical, with all upper case before lower case).
The default value is "freq" .
|
allow.partial.missing |
Logical value indicating whether a
genotype is permitted to be partially missing. When
allow.partial.missing=FALSE , if any individual allele
is missing within a genotype, the entire genotype will be converted
to a missing value. When allow.partial.missing=TRUE ,
the missingness of individual alleles will be preserved. |
markerNames |
Character vector of names to use for the genotype columns. This must have the same lenght as the number of genotype columns. |
phase |
List indicating whether phase is known for each genotype column. If the list has a single logical entry, this will apply to all genotype columns. |
... |
Optional arguments. |
An S4 object of class geneSet
Gregory R. Warnes greg@random-technologies-llc.com
## Create a test data set where there are several genotypes in columns ## of the form "A/T". test1 <- data.frame(Tmt=sample(c("Control","Trt1","Trt2"),20, replace=TRUE), G1=sample(c("A/T","T/T","T/A",NA),20, replace=TRUE), N1=rnorm(20), I1=sample(1:100,20,replace=TRUE), G2=paste(sample(c("134","138","140","142","146"),20, replace=TRUE), sample(c("134","138","140","142","146"),20, replace=TRUE), sep=" / "), G3=sample(c("A /T","T /T","T /A"),20, replace=TRUE), comment=sample(c("Possible Bad Data/Lab Error",""),20, rep=TRUE) ) test1 ## now automatically convert genotype columns geno1 <- as.geneSet(test1) geno1