tcR (version 1.3)

clonal.space.homeostasis: Clonal space homeostasis.

Description

Compute clonal space homeostatsis - statistics of how many space occupied by clones with specific proportions.

Usage

clonal.space.homeostasis(.data, .clone.types = c(Rare = 1e-05, Small = 1e-04,
  Medium = 0.001, Large = 0.01, Hyperexpanded = 1),
  .prop.col = "Read.proportion")

Arguments

.data

Cloneset data frame or list with such data frames.

.clone.types

Named numeric vector.

.prop.col

Which column to use for counting proportions.

See Also

vis.clonal.space

Examples

data(twb)
# Compute summary space of clones, that occupy
# [0, .05) and [.05, 1] proportion.
clonal.space.homeostasis(twb, c(Low = .05, High = 1)))
#        Low (0 < X <= 0.05) High (0.05 < X <= 1)
# Subj.A           0.9421980           0.05780198
# Subj.B           0.9239454           0.07605463
# Subj.C           0.8279270           0.17207296
# Subj.D           1.0000000           0.00000000
# I.e., for Subj.D sum of all read proportions for clones
# which have read proportion between 0 and .05 is equal to 1.