countClones - 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_id",
remove_na = TRUE
)
Arguments¶
- data
- data.frame with columns containing clonal assignments.
- groups
- character vector defining
data
columns containing grouping variables. Ifgroups=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. - remove_na
- removes rows with
NA
values in the clone column ifTRUE
and issues a warning. Otherwise, keeps those rows and considersNA
as a clone in the final counts and relative abundances.
Value¶
A data.frame summarizing clone counts and frequencies with columns:
clone_id
: clone identifier. This is the default column name, specified withclone='clone_id'
. If the function call uses Change-O formatted data andclone='CLONE'
, this column will have nameCLONE
.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 thecopy
column. Only present if thecopy
argument is specified.copy_freq
: frequency of the clone as a fraction of the total copy number within each group. Only present if thecopy
argument is specified.
Also includes additional columns specified in the groups
argument.
Examples¶
# Without copy numbers
clones <- countClones(ExampleDb, groups="sample_id")
# With copy numbers and multiple groups
clones <- countClones(ExampleDb, groups=c("sample_id", "c_call"), copy="duplicate_count")