Usage
shared.repertoire(.datalist, .type = 'avc', .min.ppl = 1, .head = -1,
.clear = T, .verbose = T, .by.col = '', .sum.col = '',
.max.ppl = length(.datalist))shared.matrix(.shared.rep)
Arguments
.datalist
List with data frames.
.type
String of length 3 denotes how to create a shared repertoire. See "Details" for
more information. If supplied, than parameters .by.col
and .sum.col
will be ignored. If not supplied, than columns
in .by.col
and
.min.ppl
At least how many people must have a sequence to leave this sequence in the shared repertoire.
.head
Parameter for the head
function, applied to all data frames before clearing.
.clear
If T than remove all sequences which have symbols "~" or "*" (i.e., out-of-frame sequences for amino acid sequences).
.verbose
If T than output progress.
.by.col
Character vector with names of columns with sequences and their parameters (like segment) for using for creating a shared repertoire.
.sum.col
Character vector of length 1 with names of the column with count, percentage or any other numeric chaaracteristic of sequences for using for creating a shared repertoire.
.max.ppl
At most how many people must have a sequence to leave this sequence in the shared repertoire.
.shared.rep
Shared repertoire.