Usage
buildSNPannotation(pkg, rs = TRUE, allele = TRUE, gene = TRUE,
chromosome = FALSE, position = FALSE, strand = FALSE, cytoband = FALSE,
max.genes = 0, lib.loc = NULL, others = NULL, subset = NULL,
pattern = NULL, na.rm = TRUE)Arguments
pkg
the name of the metadata package from which the data frame containing the
annotations of the SNPs should be generated.
rs
should the RefSNP-ID of the SNPs be added to the data frame?
allele
should the two alleles of each SNP be added to the data frame?
gene
should the genes associated with the SNPs be added to the data frame?
chromosome
should the chromosome to which the respective SNP belongs be added to the data frame?
position
should the physical positions of the SNPs be added to the data frame?
strand
should the strands be added to the data frame?
cytoband
logical indicating whether the cytoband of each SNP is added to the data frame.
max.genes
integer specifying the maximum number of genes associated with the respective
SNP that should be stored in the data frame. By default, all entries are considered. The corresponding column
of the data frame can also be shortened afterwards using
lib.loc
the directory in which the metadata package is stored. Needs only to be specified
if it is not stored in the usual directory of the packages.
others
character string or vector naming other entries of the object featureSet
saved in pkg that should be added to the data frame.
subset
character string consisting of the probe set IDs of the SNPs for which the data
frame should be generated. The data frame will contain all SNPs if subset = NULL
pattern
character string specifying the pattern of the probe set IDs of the SNPs for which
the data frame should be generated. For example, pattern = "SNP%" will lead to a
data frame containing all SNPs whose probe set ID start with "SNP".
na.rm
should the rows of the data frame corresponding to SNPs specified by subset
for which no information is available in the metadata package be removed?