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

In SIM: Integrated Analysis on two human genomic datasets

Description

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

Usage

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 [e-mail]

See Also

RESOURCERER.annotation.to.ID

Examples

# 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)

SIM documentation built on Nov. 8, 2020, 4:58 p.m.