est_ptr_on: Tries up to max_attempts times to compare each permutation of...

In demic: Dynamic Estimator of Microbial Communities

Tries up to max_attempts times to compare each permutation of removing random subsets of contigs/samples from X, and returns the PTR estimate if a valid one comes back from the comparisons

Description

Requires a minimum of 2 * num_subsets contigs/samples

Usage

est_ptr_on(X, subset_on, max_attempts = 10, num_subsets = 3, cor_cutoff = 0.98)

Arguments

X	cov3 dataframe
subset_on	either "contig" or "sample"
max_attempts	max number of attempts to find a valid ptr estimate
num_subsets	number of subsets to split contigs/samples into
cor_cutoff	minimum correlation coefficient to accept PTR estimate

Value

est_ptrs dataframe on success, null otherwise

• est_ptr: estimated PTR values

• coefficient: coefficient of linear regression

• pValue: p-value of linear regression

• cor: correlation coefficient

• correctY: corrected coverage

Examples

est_ptrs_001_on_contigs <- est_ptr_on(max_bin_003, "contig", num_subsets = 5)
est_ptrs_001_on_contigs

est_ptrs_001_on_samples <- est_ptr_on(max_bin_003, "sample")
is.null(est_ptrs_001_on_samples)

demic documentation built on May 29, 2024, 10:05 a.m.