fixed more typos

bin/reduce_sequence.R

@@ -3,7 +3,7 @@ library("optparse")
 
 option_list <- list(
   make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Last column must be sequences.", metavar = "character"),
-  make_option(opt_str = c("-k", "--kmer"), default = 10, help = "k-mer length. Default = %default", metavar = "integer"),
+  make_option(opt_str = c("-k", "--kmer"), default = 10, help = "K-mer length. Default = %default", metavar = "integer"),
   make_option(opt_str = c("-m", "--motif"), default = 10, help = "Estimated motif length. Default = %default", metavar = "integer"),
   make_option(opt_str = c("-o", "--output"), default = "reduced.bed", help = "Output file. Default = %default", metavar = "character"),
   make_option(opt_str = c("-t", "--threads"), default = 1, help = "Number of threads to use. Use 0 for all available cores. Default = %default", metavar = "integer"),
@@ -28,7 +28,7 @@ opt <- parse_args(opt_parser)
 #' @param output Output file. Default = reduced.bed
 #' @param threads Number of threads to use. Default = 1. Use 0 for all cores.
 #' @param clean Delete all temporary files.
-#' @param minoverlap_kmer Minimum required overlap between k-mer. Used to create reduced sequence ranges out of merged k-mer. Can not be greater than k-mer length . Default = kmer - 1
+#' @param minoverlap_kmer Minimum required overlap between k-mer. Used to create reduced sequence ranges out of merged k-mer. Can not be greater than k-mer length. Default = kmer - 1
 #' @param minoverlap_motif Minimum required overlap between motif and k-mer to consider k-mer significant. Used for k-mer cutoff calculation. Can not be greater than motif and k-mer length. Default = ceiling(motif / 2)
 #' @param min_seq_length Remove sequences below this length. Defaults to the maximum value of motif and k-mer and can not be lower.
 #' @param motif_occurrence Define how many motifs are expected per sequence. This value is used during k-mer cutoff calculation. Default = 1 meaning that there should be approximately one motif per sequence.