ScanAnnotationDataFrame-class: Class ScanAnotationDataFrame

In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description

The ScanAnnotationDataFrame class stores annotation data associated with subjects in a genotyping study, where there may be multiple scans per subject, as well as metadata describing each column. It extends the AnnotatedDataFrame class.

Extends

AnnotatedDataFrame

Constructor

ScanAnnotationDataFrame(data, metadata):

data must be a data.frame containing the scan annotation. It must contain at least the following column:

• "scanID": vector containing unique scan ids.

If a column representing sex is present, it must have the following format:

• "sex": character vector with values 'M' or 'F'.

metadata is an optional data.frame containing a description for each column in data. It should contain a column "labelDescription", with row.names(metadata) == names(data).

The ScanAnnotationDataFrame constructor creates and returns a ScanAnnotationDataFrame instance.

Accessors

In the code snippets below, object is a ScanAnnotationDataFrame object.

getScanID(object, index): A unique vector of scan IDs. The optional index is a logical or integer vector specifying elements to extract.

getSex(object, index): A character vector of sex, with values 'M' or 'F'. The optional index is a logical or integer vector specifying elements to extract.

hasSex(object): Returns TRUE if the column 'sex' is present in object.

getVariable(object, varname, index): A vector of the column varname. The optional index is a logical or integer vector specifying elements to extract. If varname is itself a vector, returns a data.frame. Returns NULL if varname is not found in object.

hasVariable(object, varname): Returns TRUE if varname is a column in object, FALSE if not.

getVariableNames(object): Returns a character vector with the names of all columns in object.

getAnnotation(object): Returns all annotation variables as a data frame.

getMetadata(object): Returns metadata describing the annotation variables as a data frame.

Inherited methods from AnnotatedDataFrame:

varLabels(object): Returns a character vector with the names of all columns in object.

pData(object): Returns all annotation variables as a data frame, or sets the annotation variables with pData(object) <- df.

varMetadata(object): Returns metadata describing the annotation variables as a data frame, or sets the metadata with varMetadata(object) <- df.

The operators $ and [ work just as they do in standard data frames, for both retrieval and assignment.

Author(s)

Stephanie Gogarten

See Also

AnnotatedDataFrame, SnpAnnotationDataFrame, GenotypeData, IntensityData

Examples

library(GWASdata)
data(illumina_scan_annot)
scanAnnot <- ScanAnnotationDataFrame(illumina_scan_annot)

scanID <- getScanID(scanAnnot)
sex <- getSex(scanAnnot)
if (hasVariable(scanAnnot, "plate")) plate <- getVariable(scanAnnot, "plate")
subjectID <- getVariable(scanAnnot, "subjectID", index=(sex == "M"))

# list columns
varLabels(scanAnnot)

# add metadata
meta <- varMetadata(scanAnnot)
meta["scanID", "labelDescription"] <- "unique scan ID"
varMetadata(scanAnnot) <- meta

# display data
head(pData(scanAnnot))

# standard operators
scanID <- scanAnnot$scanID
sex <- scanAnnot[["sex"]]
subset <- scanAnnot[1:10, 1:5]
scanAnnot$newVar <- rep(1, nrow(scanAnnot))

# replace data
df <- pData(scanAnnot)
pData(scanAnnot) <- df

amstilp/GWASTools documentation built on May 10, 2019, 1:08 a.m.