rankingRcisTarget-class {RcisTarget} | R Documentation |
This class contains the rankings used by RcisTarget.
They 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.
Class slots:
rankings: data.frame containing the rankings
colType: 'gene'or 'region'
rowType: 'motif' or the type of feature is stored (e.g. ChipSeq)
org: human/mouse/fly
genome: hg19, mm9, ...
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.
description: global description, summary, or any other information
maxRank: Maximum ranking included in the database, higher values are converted to Inf.
Note that the main slot is @rankings
,
which is the one used by RcisTarget
(it can accessed with getRanking()
).
The 'description' slots are mostly for user convenience.
## S4 method for signature 'rankingRcisTarget' show(object) ## S4 method for signature 'rankingRcisTarget' getRanking(object) ## S4 method for signature 'rankingRcisTarget' nrow(x) ## S4 method for signature 'rankingRcisTarget' ncol(x) ## S4 method for signature 'rankingRcisTarget' getMaxRank(x) ## S4 method for signature 'rankingRcisTarget' getNumColsInDB(x)
object |
[method: show] rankingRcisTarget object to show |
x |
[several methods] rankingRcisTarget object to apply the method |
show: Prints a summary of the object
getRanking: Returns the rankings
ncol, nrow: Returns the number of columns or rows of the ranking
## Loading from a .feather file: # dbFile <- "hg19-500bp-upstream-7species.mc9nr.feather" # motifRankings <- importRankings(dbFile) # motifRankings ## Loading a built object: library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp) data("hg19_500bpUpstream_motifRanking_cispbOnly") hg19_500bpUpstream_motifRanking_cispbOnly class(hg19_500bpUpstream_motifRanking_cispbOnly)