create_data: Simulate sequencing data obtained from the alphabetr approach...

In edwardslee/alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Description

create_data() simulates an alphabetr sequencing experiment by sampling clones from a clonal structure specified by the user. The clones are placed on a frequency distribution where a fixed number clones represents the top proportion of the population in frequency and the other clones represent the rest of the population in frequency. Different error models and different sampling strategies can be simulated as well.

Usage

create_data(TCR, plates, error_drop, error_seq, error_mode, skewed, prop_top,
  dist = "linear", numb_cells)

Arguments

TCR	The specified clonal structure, which can be created from create_clones.
plates	The number of plates of data.
error_drop	A vector of length 2 with the mean of the drop error rate and the sd of the drop error rate.
error_seq	A vector of length 2 with the mean of the in-frame error rate and the sd of the in-frame error rate.
error_mode	A vector of two strings determining the "mode" of the error models. The first element sets the mode of the drop errors, and the second element sets the mode of the in-frame errors. The two modes available are "constant" for a constant error rate and "lognormal" for error rates drawn from a lognormal distribution. If the mode is set to "constant" the sd specified in error_drop and/or error_seq will be ignored.
skewed	Number of clones represent the top proportion of the population by frequency (which is specified by prop_top).
prop_top	The proportion of the population in frequency represented by the number of clones specified by skewed.
dist	The distribution of frequency of the top clones. Currently only "linear" is available.
numb_cells	A two column matrix determining the sampling strategy of the experiment. The first column represents the number of cells per well, and the second column represents the number of wells with that sample size. The sum of column 2 should equal 96 times the number of plates.

Value

A list of length 2. The first element is a matrix representing the data of the alpha chains, and the second element is a matrix representing the data of beta chains. The matrix represents the sequencing data by representing the wells of the data by rows and the chain indices by column. Entry [i, j] of the matrix represents if chain j is found in well i (yes == 1, no == 0). e.g. if alpha chain 25 is found in well 10, then [10, 25] of the alpha matrix will be 1.

Examples

 # see the help for create_clones() for details of this function call
 clones <- create_clones(numb_beta = 1000,
                         dual_alpha = .3,
                         dual_beta = .06,
                         alpha_sharing = c(0.80, 0.15, 0.05),
                         beta_sharing  = c(0.75, 0.20, 0.05))

 # creating a data set with 5 plates, lognormal error rates, 10 clones
 # making up the top 60% of the population in frequency, and a constant
 # sampling strategy of 50 cells per well for 480 wells (five 96-well plates)
 dat <- create_data(clones$TCR, plate = 5,
                    error_drop = c(.15, .01),
                    error_seq  = c(.05, .001),
                    error_mode = c("lognormal", "lognormal"),
                    skewed = 10,
                    prop_top = 0.6,
                    dist = "linear",
                    numb_cells = matrix(c(50, 480), ncol = 2))

edwardslee/alphabetr documentation built on May 15, 2019, 11:03 p.m.