comb_gen: Calculate unique combinations of samples at varying replicate...

In zshao1/ERSSA: Empirical RNA-seq Sample Size Analysis

Calculate unique combinations of samples at varying replicate number

Description

comb_gen function takes the list of samples in each condition and generate unique combination of sample names that allow subsampling at varying replicate numbers.

Usage

comb_gen(condition_table = NULL, n_repetition = 30)

Arguments

condition_table	A condition table with two columns and each sample as a row. Column 1 contains sample names and Column 2 contains sample condition (e.g. Control, Treatment).
n_repetition	The number of maximum unique combinations to generate at each replicate level. More tests will be performed with a bigger value, but run time also increases linearly. Default set to 30 unique combinations.

Details

At each replicate number (2 to N-1), the total number of unique combination of samples is computed. For example, 10 condition A samples subsampled at replicate number of 2 has 45 unique combinations.

When the total number of possible combinations at a particular replicate number is more than the specified x number of repetition (default=30), then only x unique combinations are selected.

When the total number of possible combination is smaller than the specified x number of repetitions, then only unique combinations are selected. For example, 10 samples subsample for 9 replicates has 10 unique combinations and only 10 combinations will be selected instead of 30.

This is repeated for both conditions and another level of combination is performed to combine samples from the two conditions. Again, only x number of unique combinations selected. When total unique combination is smaller than x, then all unique combinations are selected.

Selected combinations of samples at each replicate number are then returned.

Value

A list of character vectors containing sample combinations. Each element in the list corresponds to a replicate level. Each combination within the character vector is a single string with sample names separated by semicolon.

Author(s)

Zixuan Shao, [e-mail]

Examples

# Use example condition_table
# example dataset containing 1000 genes, 4 replicates and 5 comb. per rep.
# level
data(condition_table.partial, package = "ERSSA")

combinations.partial = comb_gen(condition_table.partial, n_repetition=5)

zshao1/ERSSA documentation built on July 19, 2023, 9:20 p.m.