loadmirnapathways {miRNApath} | R Documentation |
This method loads associations between genes and the pathways to which they belong.
loadmirnapathways(mirnaobj, pathwayfile, genecol="Entrez Gene ID", pathwaycol="PATHWAY", columns=c(), pathwayidcol=NA)
mirnaobj |
An object of type mirnapath containing data resulting from
the loadmirnapath method.
|
pathwayfile |
The file containing the gene to pathway associations. |
genecol |
The name of the column header which contains the gene names associated with pathway data. |
pathwaycol |
The name of the column header which contains the pathway names. |
columns |
The names of any additional columns in the file being read which should equate with the mirnapath object. |
pathwayidcol |
The (optional) column header for IDs associated with the pathway names. |
The data loaded is expected to have gene names which exactly
match those gene names loaded by loadmirnatogene
.
The method returns an object of type mirnapath, a list with components:
mirnaTable |
data.frame containing the miRNA results data |
columns |
list containing the names of required column headers associated to the actual column header supplied in the dataset contained in mirnaTable. Required headers: mirnacol, assayidcol. Optional headers: groupcol, pvaluecol, foldchangecol, expressioncol, filterflagcol |
groupcount |
the number of groups contained in mirnaTable using the groupcol, if supplied |
state |
the current state of the object, using the following values in order of progress through the typical workflow: unfiltered, filtered, enriched. |
James M. Ward jmw86069@gmail.com
John Cogswell (2008) Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways, Journal of Alzheimer's Disease 14, 27-41.
loadmirnapath
,
filtermirnapath
,
loadmirnatogene
,
loadmirnapathways
,
runEnrichment
## Load miRNA expression data from AD miRNA paper ## This data contains miRNA expression data, data(mirnaobj); ## Write a file as example of required input write.table(mirnaobj@mirnaPathways, file = "mirnaPathways.txt", quote = FALSE, row.names = FALSE, col.names = TRUE, na = "", sep = "\t"); ## Load the gene to pathway associations mirnaobj <- loadmirnapathways( mirnaobj = mirnaobj, pathwayfile = "mirnaPathways.txt", pathwaycol = "Pathway Name", genecol = "Entrez Gene ID"); ## Display summary, noting the number of genes reported mirnaobj;