estimate_hopping_rate: Step 4: estimate the sample index hopping rate (SIHR)

In csglab/PhantomPurgeR: PhantomPurgeR

Step 4: estimate the sample index hopping rate (SIHR)

Description

Step 4: estimate the sample index hopping rate (SIHR)

Usage

estimate_hopping_rate(out, max_r = NULL)

Arguments

out	A list out containing read_counts and sample_names.
max_r	Maximum PCR duplication level to consider. The default considers all observed levels.

Details

Given that the number of observations in the joined read counts datatable tends to be in the hundreds of millions, observations with similar outcomes are tallied to produce an outcome counts datatable which in turn is used to create a chimera counts datatable that tallies the number of chimeric and tho non-chimeric at each PCR duplication level r. The chimera counts datatable is then used as input to the GLM Model in order to estimate, from the proportion of chimeric observations, the sample index hopping rate. A list of summary statistics is also returned containing the conditional and marginal distributions of reads, and the proportion of molecules across samples \pi_r for each each PCR duplication level r.

Value

A list out with a total of 6 elements: read_counts, sample_names, outcome_counts, glm estimates, chimera counts, and summary_stats.

csglab/PhantomPurgeR documentation built on July 27, 2023, 8:05 a.m.