From 2ea0ca44eb38e439ae8318eb0addadc231d8ad54 Mon Sep 17 00:00:00 2001
From: HajkD <hajkdrost@googlemail.com>
Date: Thu, 5 Sep 2019 22:01:50 +0100
Subject: [PATCH] When 'replace = FALSE'  is set in
 extract_random_seqs_from_genome(), the command will still hold 'replace =
 TRUE' for the chromosome and strand to be sampled, but the sequence that was
 sampled will be removed #2

---
 R/extract_random_seqs_from_genome.R | 10 +++++++---
 R/sample_chromosome_intervals.R     | 18 +++++++++++++++---
 man/sample_chromosome_intervals.Rd  |  7 ++++++-
 3 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/R/extract_random_seqs_from_genome.R b/R/extract_random_seqs_from_genome.R
index d5f9faa..914a1e6 100644
--- a/R/extract_random_seqs_from_genome.R
+++ b/R/extract_random_seqs_from_genome.R
@@ -79,7 +79,7 @@ extract_random_seqs_from_genome <-
         res <- vector("list", length(size))
         
         for (i in seq_len(size)) {
-          sample_chromsome <- sample.int(length(chr_names), 1, replace = replace, prob = prob)
+          sample_chromsome <- sample.int(length(chr_names), 1, replace = TRUE, prob = NULL)
           sample_strand <- sample.int(2, 1, replace = replace, prob = c(0.5, 0.5))
           
           if (sample_strand == 1){
@@ -87,7 +87,9 @@ extract_random_seqs_from_genome <-
               chr_size = imported_genome_i[chr_names[sample_chromsome]]@ranges@width,
               interval_width = interval_width,
               strand = "plus",
-              size = 1
+              size = 1,
+              replace = replace,
+              prob = prob
             )
             
             sample_i <- dplyr::mutate(sample_i, chr = chr_names[sample_chromsome])
@@ -99,7 +101,9 @@ extract_random_seqs_from_genome <-
               chr_size = imported_genome_i[chr_names[sample_chromsome]]@ranges@width,
               interval_width = interval_width,
               strand = "minus",
-              size = 1
+              size = 1,
+              replace = replace,
+              prob = prob
             )
             
                 sample_i <-
diff --git a/R/sample_chromosome_intervals.R b/R/sample_chromosome_intervals.R
index 42fa648..1f42623 100644
--- a/R/sample_chromosome_intervals.R
+++ b/R/sample_chromosome_intervals.R
@@ -10,9 +10,17 @@
 #' \item \code{strand = "minus"}
 #' }
 #' @param size a non-negative integer giving the number of sequences that shall be sampled from random genomic loci.
+#' @param replace logical value indicating whether sampling should be with replacement. Default: \code{replace = TRUE}.
+#' @param prob a vector of probability weights for obtaining the elements of the vector being sampled. Default is \code{prob = NULL}.
 #' @author Hajk-Georg Drost
-sample_chromosome_intervals <- function(chr_size, interval_width, strand, size) {
-  
+sample_chromosome_intervals <-
+  function(chr_size,
+           interval_width,
+           strand,
+           size,
+           replace = TRUE,
+           prob = NULL) {
+    
   if (!is.element(strand, c("plus", "minus")))
     stop("The 'strand' argument can only be specified as strand = 'plus' or strand = 'minus'.", call. = FALSE)
   
@@ -27,7 +35,11 @@ sample_chromosome_intervals <- function(chr_size, interval_width, strand, size)
     }
   
   # random start position in chromosome
-  random_start <- sample.int(ifelse((chr_size - interval_width) == 0,1, chr_size - interval_width), size)
+    random_start <-
+      sample.int(ifelse((chr_size - interval_width) == 0, 1, chr_size - interval_width),
+                 size,
+                 replace = replace,
+                 prob = prob)
   # compute random end position in chromosome given interval width
   random_end <- random_start + interval_width - 1
   
diff --git a/man/sample_chromosome_intervals.Rd b/man/sample_chromosome_intervals.Rd
index e7c8ee0..3cb1ca0 100644
--- a/man/sample_chromosome_intervals.Rd
+++ b/man/sample_chromosome_intervals.Rd
@@ -4,7 +4,8 @@
 \alias{sample_chromosome_intervals}
 \title{Helper function to sample random intervals of length \code{interval_width} from chromosomes}
 \usage{
-sample_chromosome_intervals(chr_size, interval_width, strand, size)
+sample_chromosome_intervals(chr_size, interval_width, strand, size,
+  replace = TRUE, prob = NULL)
 }
 \arguments{
 \item{chr_size}{an integer value defining the length of the chromosome.}
@@ -19,6 +20,10 @@ are:
 }}
 
 \item{size}{a non-negative integer giving the number of sequences that shall be sampled from random genomic loci.}
+
+\item{replace}{logical value indicating whether sampling should be with replacement. Default: \code{replace = TRUE}.}
+
+\item{prob}{a vector of probability weights for obtaining the elements of the vector being sampled. Default is \code{prob = NULL}.}
 }
 \description{
 This function samples a random locus given the chromosome lenght (\code{chr_size})