compare_genome_stats: Compare user-defined assembly statistics with statistics of...

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Compare user-defined assembly statistics with statistics of NCBI genomes

Description

This function helps users analyze their genome assembly stats in a context by comparing metrics obtained by users with "reference" metrics in closely-related organisms.

Usage

compare_genome_stats(ncbi_stats = NULL, user_stats = NULL)

Arguments

ncbi_stats

A data frame of summary statistics for a particular taxon obtained from the NCBI, as obtained with the function get_genome_stats.

user_stats

A data frame with assembly statistics obtained by the user. A column named accession is mandatory, and it must contain unique identifiers for the genome(s) analyzed by the user. Dummy variables can be used as identifiers (e.g., "my_genome_001"), as long as they are unique. All other column containing assembly stats must have the same names as their corresponding columns in the data frame specified in ncbi_stats. For instance, stats on total number of genes and sequence length must be in columns named "gene_count_total" and "sequence_length", as in the ncbi_stats data frame.

Details

For each genome assembly statistic (e.g., "gene_count_total"), values in user_stats are compared to a distribution of values from ncbi_stats, and their percentile and rank in the distributions are reported.

Value

A data frame with the following variables:

accession

character, unique identifier as in user_stats$accession.

variable

character, name of the genome assembly metric (e.g., "CC_ratio").

percentile

numeric, percentile in the distribution.

rank

numeric, rank in the distribution (highest to lowest). For the variable "CC_ratio", ranks go from lowest to highest.

Examples

# Use case: user assembled a maize (Zea mays) genome

## Obtain stats for maize genomes on the NCBI
ncbi_stats <- get_genome_stats(taxon = "Zea mays")

## Create a data frame of stats for fictional maize genome
user_stats <- data.frame(
    accession = "my_lovely_maize",
    sequence_length = 2.4 * 1e9,
    gene_count_total = 50000,
    CC_ratio = 1
)

# Compare stats
compare_genome_stats(ncbi_stats, user_stats)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.