A package to facilitate building and analyzing networks of T cell receptors to help better understand clonality, antigen specificity, and other immunological questions.
Open an R session, and execute the following code:
if (!require("devtools")) install.packages("devtools")
devtools::install_github("BenaroyaResearch/tcrGraph", build_vignettes = TRUE)
The following R packages will be automatically installed if necessary: stringr, dplyr, magrittr, rlang, igraph, httr
This package includes an introductory vignette demonstrating basic use of the package functions. To view this vignette, execute the following R code:
vignette("tcrGraphIntro", "tcrGraph")
-
tcrGraph
- An S3 class, with implementations of methods
print
,plot
, andis.tcrGraph
. Generally you should create atcrGraph
object using the functionmakeTcrGraph()
.
- An S3 class, with implementations of methods
-
makeTcrGraph(tcrDf, link = "full_nt_sequence")
- Accepts a data frame of TCR information, with columns for libid, v_gene, j_gene, and the column indicated by the link argument. Returns a tcrGraph object.
-
getClonesFromTcrGraph(tcrData, maxA = 2, maxB = 2, maxD = -1, maxG = -1, format = "compressed", link = "full_nt_sequence")
- Accepts either a tcrGraph object or a data frame that can be used to construct a tcrGraph object. Generates summary information about the frequencies of the clones in the dataset. A 'clone' is defined as a maximal subgraph containing at most the number of alpha, beta, delta, and gamma chains set by
maxA
,maxB
,maxD
, andmaxG
.
- Accepts either a tcrGraph object or a data frame that can be used to construct a tcrGraph object. Generates summary information about the frequencies of the clones in the dataset. A 'clone' is defined as a maximal subgraph containing at most the number of alpha, beta, delta, and gamma chains set by