SeqVarData-class: SeqVarData

In SeqVarTools: Tools for variant data

Description

Extends SeqVarGDSClass to include annotation for samples and variants.

Details

A SeqVarData object adds an AnnotatedDataFrame for both samples and variants to a SeqVarGDSClass object.

Note that a SeqVarData object must be created using an unfiltered SeqVarGDSClass object. The sample.id column in the sampleData AnnotatedDataFrame must exactly match the sample.id node in the GDS file (and similarly for variant.id in variantData). This enables all subsequent filters set on the SeqVarData object to apply to the GDS and the annotation simultaneously.

Constructor

SeqVarData(gds, sampleData, variantData): Returns a SeqVarData object.

gds can be either the filename of a sequencing GDS file or an existing SeqVarGDSClass object.

sampleData must be an AnnotatedDataFrame with a column sample.id matching sample.id in the GDS file. If this argument is missing, a data frame with 0 columns will be created.

variantData must be an AnnotatedDataFrame with a column variant.id matching variant.id in the GDS file. If this argument is missing, a data frame with 0 columns will be created.

Accessors

sampleData(x), sampleData(x)<- value: Get or set the AnnotatedDataFrame with sample data. If a sample filter has been applied with seqSetFilter, only selected samples will be returned. value must include all samples.

variantData(x), variantData(x)<- value: Get or set the AnnotatedDataFrame with variant data. If a variant filter has been applied with seqSetFilter, only selected variants will be returned. value must include all variants.

granges(x): Return a GRanges object with the columns of variantData as metadata columns.

validateSex(x): Return the contents of a column named "sex" in sampleData(x), provided the contents are valid (values either "M"/"F" or 1/2, or NA). If the column is missing or invalid, return NULL.

See SeqVarGDSClass for additional methods.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, seqVCF2GDS, seqOpen, seqGetData, seqSetFilter, seqApply, seqClose

Examples

gds <- seqOpen(seqExampleFileName("gds"))

## create sample annotation
library(Biobase)
sample.id <- seqGetData(gds, "sample.id")
sex <- sample(c("M","F"), length(sample.id), replace=TRUE)
phenotype <- rnorm(length(sample.id), mean=10)
samp <- data.frame(sample.id, sex, phenotype, stringsAsFactors=FALSE)
meta <- data.frame(labelDescription=c("unique sample identifier",
     "sex (M=male, f=female)", "example phenotype"), 
      row.names=names(samp), stringsAsFactors=FALSE)
sample.data <- AnnotatedDataFrame(samp, meta)

seqData <- SeqVarData(gds, sample.data)

head(validateSex(seqData))

## add another annotation column
sample.data$site <- sample(letters, length(sample.id), replace=TRUE)
varMetadata(sample.data)["site", "labelDescription"] <- "study site"
sampleData(seqData) <- sample.data

## set a filter
seqSetFilter(seqData, sample.id=sample.id[1:10])
nrow(sampleData(seqData))

seqClose(seqData)

SeqVarTools documentation built on Nov. 22, 2020, 2 a.m.