importRankings {RcisTarget} | R Documentation |
The rankings are typically loaded from a .feather file
with importRankings()
.
If the associated .descr file is available, it will also load the description of the database.
importRankings(dbFile, columns = NULL, dbDescr = NULL)
dbFile |
.feather file containing the rankings |
columns |
Columns to import from the .feather file (e.g. only selected genes or regions) |
dbDescr |
The description fields are typically imported from the
".descr" file with the same filename as the
|
rankingRcisTarget object with the following slots: #'
rankings: data.frame containing the rankings
colType: 'gene'or 'region'
nColsInDB: Number of columns (e.g. genes/regions) available in the database (.feather file). Note that not all might be loaded in the current object.
rowType: 'motif' or the type of feature is stored (e.g. ChipSeq)
org: human/mouse/fly
genome: hg19, mm9, ...
description: global description, summary, or any other information
maxRank: Maximum ranking included in the database, higher values are converted to Inf.
## Loading from a .feather file (the .descr file is read automatically): #motifRankings<-importRankings("hg19-500bp-upstream-7species.mc9nr.feather") ## The annotations for Motif collection 9 (sufix 'mc9nr') # are already included in RcisTarget, and can be loaded with: data(motifAnnotations_hgnc) ## For other versions, import the appropiate annotation. e.g.: # annotDb <- importAnnotations("motifs-v9-nr.hgnc-m0.001-o0.0.tbl") # optional: motifsInRanking <- getRanking(motifRankings)$features