cutsite_distance: Calculate Cutsite Distance Distribution.
In angelgr2/radseq_tools: Tools for the Exploratory Analysis of RADseq Data

Description Usage Arguments Value Author(s) See Also Examples

Function to calculate inter-cutsite distances. It uses R diff() to calculate the difference between per-chromosome/scaffold cutsite positions vectors.

1	cutsite_distance(cut_list)

cut_list

List containing the per-chromosome/scaffold cutsite position vectors. Argument is designed to be compatible with the output of the find_cuts function.

Returns a numeric atomic vector of genome-wide inter-cutsite distances. It is compatible with R vector functions.

Angel G. Rivera-Colon

find_cuts

# Generate prior data
myfasta <- system.file("extdata", 
                       "test_geno.fa.gz",
                       package = "RADseqTools")
mySeqs <- process_fasta(myfasta, 10000)
myEnz <- 'CTGCAG'
cutPos <- find_cuts(mySeqs, myEnz)

#
# For this function
#

# Find cutsite distance distribution in cutPos
cutDist <- cutsite_distance(cutPos)

# Object is compatible with R vector functions
# Obtain summary statistic for the cutsite distribution vector
summary(cutDist)
mean(cutDist)
sd(cutDist)