tcR (version 2.2.4)

tailbound.proportion: Proportions of specifyed subsets of clones.

Description

Get a specifyed subset of the given repertiure and compute which proportion in counts it has comparing to the overall count.

tailbound.proportion - subset by the count;

top.proportion - subset by rank (top N clones);

clonal.proportion - subset by a summary percentage (top N clones which in sum has the given percentage).

Usage

tailbound.proportion(.data, .bound = 2, .col = 'Read.count')
top.proportion(.data, .head = 10, .col = 'Read.count')
clonal.proportion(.data, .perc = 10, .col = 'Read.count')

Arguments

.data

Data frame or a list with data frames.

.bound

Subset the .data by .col <= .bound.

.col

Column's name with counts of sequences.

.head

How many top values to choose - parameter to the .head function.

.perc

Percentage (0 - 100).

Value

For tailbound.proportion - numeric vector of percentage.

For top.proportion - numeric vector of percentage for top clones. For clonal.proportion - vector or matrix with values for number of clones, occupied percentage and proportion of the chosen clones to the overall count of clones.

See Also

vis.top.proportions, prop.sample

Examples

# NOT RUN {
                                # How many clones fill up approximately
clonal.proportion(immdata, 25)  # the 25% of the sum of values in 'Read.count'?

                                # What proportion of the top-10 clones' reads
vis.top.proportions(immdata)  # Plot this proportions.

                                # What proportion of sequences which
                                # has 'Read.count' <= 100 to the
tailbound.proportion(immdata, 100)  # overall number of reads?
# }