tcR (version 1.1)

freq.segments: V- and J-segments frequency.

Description

Get frequencies or counts of segments (V / J - usage).

Usage

freq.segments(.data, .alphabet = 'TRBV', .count = F, .meat = F, .other = T,
              .laplace = 1, .column = NULL, .sum.col = "Read.count")
freq.segments.2D(.data, .alphabet = 'beta', .count = F, .meat = F,
                 .laplace = 1, .columns = NULL, .sum.col = "Read.count", ...)
freq.Va(.data, .count = F, .meat = F, .other = T, .laplace = 1, .sum.col = "Read.count")
freq.Vb(.data, .count = F, .meat = F, .other = T, .laplace = 1, .sum.col = "Read.count")
freq.Ja(.data, .count = F, .meat = F, .other = T, .laplace = 1, .sum.col = "Read.count")
freq.Jb(.data, .count = F, .meat = F, .other = T, .laplace = 1, .sum.col = "Read.count")

Arguments

.data

Mitcr data.frame or list with data.frames.

.alphabet

Vector of elements in the alphabet for freq.segments, one of the strings 'TRBV' (for using V_BETA_ALPHABET variable, that user should load before calling functions (same for other strings)), 'TRAV', 'TRBJ', 'TRAJ' for V- and J-segments alphabets for freq.

.count

Should we return count or percentage?

.meat

Compute statistics using counts of elements (e.g., Read.count) or not.

.other

Should elements not in the given alphabet be shown in the result matrix.

.laplace

Value for the Laplace correction.

.column,.columns

Column's name with elements from the given alphabet for the freq.segments or a character vector of length two for freq.segments.2D.

.sum.col

Which column use to count frequencies if .meat = T. Default: 'Read.count'.

...

Don't use it, for internal purpose.

Value

• Data.frame with columns Segments and their frequencies in the column Freq.

See Also

vis.V.usage vis.J.usage pca.segments

Examples

# Load your data
data(twb)
# Load human alphabets
data(human.alphabets)
# compute V-segments frequencies
seg <- freq.segments(twb)
# plot V-segments frequencies as a grid
vis.grid.stats(seg)
# plot V-segments frequencies from the data
vis.V.usage(twb)