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Extract public sequences

Source: R/basicFunctions.R
getPublic.Rd

This function allows to subset a RepSeqExperiment object in order to keep sequences that are shared by at least two samples:

- belonging to a specified group

- within the whole dataset

Usage

getPublic(x, level = c("ntCDR3", "aaCDR3", "ntClone", "aaClone"), group = NULL)

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

a vector of character indicating the group column name in the mData slot and one experimental group within this column.

Samples belonging to the chosen experimental group will be analyzed. The column must be of class factor.

Default is NULL, the analysis is performed on the whole dataset.

Value

an object of class RepSeqExperiment composed exclusively of shared sequences between the specified samples.

Examples


data(RepSeqData)

publicSeq <- getPublic(x = RepSeqData,
                             level = "aaClone",
                             group = c("cell_subset", "amTreg"))