link.metadata: Link a metadata annotation file to expression ID

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/link.metadata.R

Description

Get annotation out of a AnnotationData package and link them to the expression data using the expression probe ID's

Usage

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link.metadata(data = expr.data, 
              col.ID.link = 1, 
              chr = as.list(hgu133plus2CHR), 
              chrloc = as.list(hgu133plus2CHRLOC), 
              symbol = as.list(hgu133plus2SYMBOL))

Arguments

data

data.frame with expression data including an expression probe ID column.

col.ID.link

numeric value, specifying the column of data that contains the ID to link with the poslist.

chr

list specifying the metadata annotation of the chromosome location on the genome.

chrloc

list specifying the metadata annotation of the location of the probe on the chromosome.

symbol

list specifying the metadata annotation of the symbol corresponding to the probe.

Details

Often, the annotation for expression array probes lack chromosome position information. Therefore, this function adds the two required columns to run the integrated.analysis: "CHROMOSOME" and "STARTPOS". In addition, the optional column, "Symbol" is added.

Value

A data.frame is returned, containing a dataset with annotation columns which can be used forintegrated.analysis.

Author(s)

Marten Boetzer, Melle Sieswerda, Renee x Menezes [email protected]

See Also

RESOURCERER.annotation.to.ID

Examples

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# first download and install the AnnotationData package for your expression array platform
# for example
## Not run: library(hgu133plus2)
## Not run: expr.data <- link.metadata(data, col.ID.link = 1, chr = as.list(hgu133plus2CHR), 
chrloc = as.list(hgu133plus2CHRLOC), symbol = as.list(hgu133plus2SYMBOL))
## End(Not run)

Bioconductor-mirror/SIM documentation built on June 1, 2017, 1:15 a.m.