Description Usage Arguments Details Value Author(s) Examples
View source: R/findSynexprsStep.R
Internal function - finds the synexpression groups for a single given pathway.
1 | findOnepwaySynexprs(myIDs, myDataSet, cellTypeTag, min.clustersize = 5, removeGenes = NULL, ...)
|
myIDs |
a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed or a character codevector of gene names of a pathway. |
myDataSet |
|
cellTypeTag |
character string of the variable name which stores the cell-lineages or experimental groups of interest for the samples in the data set (this string should be one of the column names of pData(myEset)). |
min.clustersize |
integer specifying the minimum number of genes that must be present in clusters that are inferred. |
removeGenes |
|
... |
additional arguments. |
This function is called internally by calcFuncSynexprs
. Users should use calcFuncSynexprs
rather than calling findOnepwaySynexprs
directly.
A SynExpressionSet
object is returned.
Jessica Mar
1 2 3 4 5 6 7 8 9 | ## Not run:
data(subset.loring.eset)
attractor.states <- findAttractors(subset.loring.eset, "celltype", nperm=10, annotation="illuminaHumanv1.db")
remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
map.syn <- findOnepwaySynexprs("04010", attractor.states, "celltype", removeGenes=remove.these.genes)
vec.geneid <- c("GI_17999531-S","GI_17978503-A")
custom.syn <- findSynexprs(vec.geneid, subset.loring.eset, "celltype", removeGenes=remove.these.genes)
## End(Not run)
|
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