Extract the most frequent sequences — getTopSequences • AnalyzAIRR

This function extracts the top n sequences within all samples or a group of samples.

Usage

getTopSequences(
  x,
  level = c("aaClone", "ntClone", "aaCDR3", "ntCDR3"),
  group = NULL,
  prop = 0.01
)

Arguments

x: an object of class RepSeqExperiment
level: a character specifying the level of the repertoire to be taken into account. Should be one of aaClone","ntClone", "ntCDR3" or "aaCDR3".
group: character, column name in mData indicating the group on which the extraction will be applied. Must be of class factor. Default is NULL.
prop: a numeric between 0 and 1 indicating the proportion of top sequences to extract.

Value

an object of class RepSeqExperiment

Examples


data(RepSeqData)
topClones <- getTopSequences(x = RepSeqData,
                          level = "aaClone",
                          group = c("cell_subset", "amTreg"), prop = 0.1)