Description Usage Arguments Value Author(s) See Also Examples
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.
1 2 3 | Per_Sample_Coverage(num_cutsites,
num_samples,
sequencing_machine = NULL)
|
num_cutsites |
Number of cutsites present in the genome. This number can be the output from |
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, |
Returns a vector with an estimate of low, medium, and high coverage.
Kira Long
1 2 3 4 5 6 7 8 | # define parameters
numberCuts <- 39000
numberSamples <- 96
#Run arguments in function
Per_Sample_Coverage(numberCuts,
numberSamples,
"hiseq2500")
|
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