group.clonotypes: Get all unique clonotypes.

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

Get all unique clonotypes with merged counts. Unique clonotypes are those with either equal CDR3 sequence or with equal CDR3 sequence and equal gene segments. Counts of equal clonotypes will be summed up.

Usage

group.clonotypes(
  .data,
  .gene.col = "V.gene",
  .count.col = "Read.count",
  .prop.col = "Read.proportion",
  .seq.col = "CDR3.amino.acid.sequence"
)

Arguments

.data	Either tcR data frame or a list with data frames.
.gene.col	Either name of the column with gene segments used to compare clonotypes or NA if you don't need comparing using gene segments.
.count.col	Name of the column with counts for each clonotype.
.prop.col	Name of the column with proportions for each clonotype.
.seq.col	Name of the column with clonotypes' CDR3 sequences.

Value

Data frame or a list with data frames with updated counts and proportion columns and rows with unique clonotypes only.

Examples

## Not run: 
tmp <- data.frame(A = c('a','a','b','c', 'a')
B = c('V1', 'V1','V1','V2', 'V3')
C = c(10,20,30,40,50), stringsAsFactors = F)
tmp
#   A  B  C
# 1 a V1 10
# 2 a V1 20
# 3 b V1 30
# 4 c V2 40
# 5 a V3 50
group.clonotypes(tmp, 'B', 'C', 'A')
#  A  B  C
#  1 a V1 30
#  3 b V1 50
#  4 c V2 30
#  5 a V3 40
group.clonotypes(tmp, NA, 'C', 'A')
#   A  B  C
# 1 a V1 80
# 3 b V1 30
# 4 c V2 40
# For tcR data frame:
data(twb)
twb1.gr <- group.clonotypes(twb[[1]])
twb.gr <- group.clonotypes(twb)

## End(Not run)

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