SeqVarData {SeqVarTools} | R Documentation

## SeqVarData

### 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)

[Package SeqVarTools version 1.30.0 Index]