NHS_10001_consensus: Output of get_consensus_df

In jkruppa/viralDetectTools: Modules for a viral detection pipeline

Description

A example output of the get_consensus_df function.

Usage

NHS_10001_consensus

Format

A list with two entries:

$consensus_df

genebank_id

Genbank ID of the reference viral strain

con_prob

Coverage probability. How unique is the base?

pos

Position on the reference

bool

Mathc between the reference and the consensus sequence

$entropy_df

genebank_id

Genbank ID of the reference viral strain

entropy

Entropy of the consensus reference

$run_len_df

genebank_id

Genbank ID of the reference viral strain

min

Minimum run of bases to the reference

first

First quartile of the runs to the reference

median

Median of the runs to the reference

mean

Mean of the runs to the reference

third

Third quartile of the runs to the reference

max

Maximum run of bases to the reference

run_to_ref

Maximal run to the reference

run_not_to_ref

Maximal run _not_ to the reference

$median_con_prob_df

genebank_id

Genbank ID of the reference viral strain

min

Minimum of the consensus_df$con_prob

first

First quartile of the consensus_df$con_prob

median

Median of the consensus_df$con_prob

mean

Mean of the consensus_df$con_prob

third

Third quartile of the consensus_df$con_prob

max

Maximum of the consensus_df$con_prob

$coverage_equal_ref_df

genebank_id

Genbank ID of the reference viral strain

coverage_equal_ref

How many of the consensus base match the reference base?

$coverage_overall_ref_df

genebank_id

Genbank ID of the reference viral strain

coverage_overall_ref

Ho much of the reference is covered by the consensus sequence

Source

ftp://ftp.ncbi.nlm.nih.gov/genbank

jkruppa/viralDetectTools documentation built on May 30, 2019, 3:41 p.m.