Per_Sample_Coverage: Estimate coverage per sample

In angelgr2/radseq_tools: Tools for the Exploratory Analysis of RADseq Data

Description

This function will calculate the predicted per-sample coverage given the number of cutsites (from previous number_cutsites()) in the genome and a user-defined number of samples. The user can also define the Illumina platform to be used, which will determine the range of raw reads used to calculate expected coverage. This function outputs a predicted range of coverages (low, medium, high) given the set range of reads that an Illumina sequencer can give per lane.

Usage

Per_Sample_Coverage(num_cutsites,
                    num_samples,
                    sequencing_machine = NULL)

Arguments

num_cutsites	Number of cutsites present in the genome. This number can be the output from number_cutsites().
num_samples	Number of samples that the user wants to sequence in a single Illumina lane.
sequencing_machine	Illumina sequencing platform that the user wants to use for sequencing. Argument has two parameters, hiseq2500 and hiseq4000, each has different read throughputs. If no machine is provided, the function will default to hiseq2500.

Value

Returns a vector with an estimate of low, medium, and high coverage.

Author(s)

Kira Long

See Also

number_cutsites

Examples

# define parameters
numberCuts <- 39000
numberSamples <- 96

#Run arguments in function
Per_Sample_Coverage(numberCuts, 
                    numberSamples,
                    "hiseq2500")

angelgr2/radseq_tools documentation built on May 15, 2019, 3:59 a.m.