R: Tabulates clones sizes

countClones {alakazam}

R Documentation

Tabulates clones sizes

Description

countClones determines the number of sequences and total copy number of clonal groups.

Usage

countClones(data, groups = NULL, copy = NULL, clone = "CLONE")

Arguments

`data`	data.frame with Change-O style columns containing clonal assignments.
`groups`	character vector defining `data` columns containing grouping variables. If `groups=NULL`, then do not group data.
`copy`	name of the `data` column containing copy numbers for each sequence. If this value is specified, then total copy abundance is determined by the sum of copy numbers within each clonal group.
`clone`	name of the `data` column containing clone identifiers.

Value

A data.frame summarizing clone counts and frequencies with columns:

CLONE: clone identifier.
SEQ_COUNT: total number of sequences for the clone.
SEQ_FREQ: frequency of the clone as a fraction of the total number of sequences within each group.
COPY_COUNT: sum of the copy counts in the copy column. Only present if the copy argument is specified.
COPY_FREQ: frequency of the clone as a fraction of the total copy number within each group. Only present if the copy argument is specified.

Also includes additional columns specified in the groups argument.

Examples

# Without copy numbers
clones <- countClones(ExampleDb, groups="SAMPLE")

# With copy numbers and multiple groups
clones <- countClones(ExampleDb, groups=c("SAMPLE", "ISOTYPE"), copy="DUPCOUNT")

[Package alakazam version 0.3.0 Index]