Description Usage Arguments Details Value Note Author(s) References See Also Examples
View source: R/PlotKmerFrequency.R
This function will utilize part of the output from both function GenomeEstimate
and FindTrustKmer
and plot the distribution of counted kmers at various frequencies.
Additionally, it will indicate the mean coverage of kmers, as well as the theoretical poisson distribution of kmer frequency with the mean of kmer coverage.
1 | PlotKmerFrequency(file, kmer_len, start_point, peak, end_point)
|
file |
Counted kmer frequency file from |
kmer_len |
The length of kmers. |
start_point |
The starting point of trusted kmers. Get this value trhough function |
peak |
The mean coverage of kmers. Get this value through function |
end_point |
The end point of single copy region. Get this value through function |
This function takes the output from jellyfish count
function and the column of the data have to be renamed into "frequency" and "counts" respectively.
The function will utilize the output (The starting point of trusted kmer, mean coverage of kmer, and ending point of single copy region) from function FindTrustKmer
and GenomeEstimate
. The theoretical poission distribution of counted kmer frequency is based on the calcualted single copy region and the mean coverage of kmer.
This function will return a plot of counted kmer frequency distribution. Function PlotKmerFrequency
also give a theoratical poisson distribution with a mean of mean coverage of kmers.
N/A
Qiong Liu
More details about calculation can be referred at:
http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html
https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/
Function FindTrustKmer
and GenomeEstimate
1 2 3 4 5 6 7 8 9 10 11 | # load an example data called b
data(b)
# Get startingpoint of trusted kmer
FindTrustKmer(b,30)
# Get the mean covergae of kmer, ending point of single copy region
GenomeEstimate(b,30)
# Plot the figure
PlotKmerFrequency(file=b,kmer_len=30,start_point = 13,peak=36,end_point = 80)
|
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