importRankings {RcisTarget} | R Documentation |
The rankings are typically loaded from a .feather or .parquet file
with importRankings()
.
importRankings( dbFile, columns = NULL, dbDescr = NULL, indexCol = "features", warnMissingColumns = TRUE ) getRowNames(dbFile) getColumnNames(dbFile)
dbFile |
.feather or .parquet file containing the rankings |
columns |
Columns to load from the .feather or .parquet file (e.g. to read only specific genes or regions) |
dbDescr |
Description fields (not used internally) e.g.:
|
indexCol |
Column name containing the feature IDs (e.g. motif names or chip-seq tracks). |
warnMissingColumns |
If 'columns' is provided, warn if any ID is not available in the rankings? |
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 or .parquet 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 or .parquet file (the .descr file is read automatically): #motifRankings<-importRankings("hg19-500bp-upstream-7species.mc9nr.feather") #motifRankings<-importRankings("hg19-500bp-upstream-7species.mc9nr.parquet") ## 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