link.metadata {SIM} | R Documentation |
Get annotation out of a AnnotationData package and link them to the expression data using the expression probe ID's
link.metadata(data = expr.data, col.ID.link = 1, chr = as.list(hgu133plus2CHR), chrloc = as.list(hgu133plus2CHRLOC), symbol = as.list(hgu133plus2SYMBOL))
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. |
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.
A data.frame
is returned, containing a dataset with annotation columns
which can be used for integrated.analysis
.
Marten Boetzer, Melle Sieswerda, Renee x Menezes R.X.Menezes@lumc.nl
# 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)