set.people.vector: Set and get attributes of a mutation network related to...

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

Set vertice attributes 'people' and 'npeople' for every vertex in the given graph. Attribute 'people' is a binary string indicating in which repertoire sequence are found. Attribute 'npeople' is a integer indicating number of repertoires, in which this sequence has been found.

Usage

set.people.vector(.G, .shared.rep)

get.people.names(.G, .V = V(.G), .paste = T)

Arguments

.G	Mutation network.
.shared.rep	Shared repertoire.
.V	Indices of vertices.
.paste	If TRUE than concatenate people names to one string, else get a character vector of names.

Value

New graph with 'people' and 'npeople' vertex attributes or character vector of length .V or list of length .V.

Examples

## Not run: 
data(twb)
twb.shared <- shared.repertoire(twb)
G <- mutation.network(twb.shared)
get.people.names(G, 300, T)  # "Subj.A|Subj.B"
get.people.names(G, 300, F)  # list(c("Subj.A", "Subj.B"))

## End(Not run)

Example output

Loading required package: ggplot2
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: gridExtra

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine

Loading required package: reshape2
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:dplyr’:

    as_data_frame, groups, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.

========================================
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! The tcR package WILL SOON BE ORPHANED 
!! AND REMOVED FROM CRAN.
!!
!! A new package is available that is 
!! designed to replace tcR: 
!! immunarch  --  https://immunarch.com/
!!
!! We will be happy to help you to move
!! to the new package. Feel free to contact us:
!! http://github.com/immunomind/immunarch
!!
!! Sincerely, 
!!  immunarch dev team and 
!!  Vadim I. Nazarov, lead developer of tcR
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=======================================

Attaching package: ‘tcR’

The following object is masked from ‘package:igraph’:

    diversity

Aggregating sequences...

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Merging data tables...

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[1] "Subj.A|Subj.B"
[[1]]
[1] "Subj.A" "Subj.B"

tcR documentation built on July 2, 2020, 3:18 a.m.