From 6cd598556ef0e0037ed2c1e0bc379703ada5dfdc Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 4 Dec 2018 13:46:10 +0100 Subject: [PATCH] added documentation --- bin/cdhit_wrapper.R | 6 +++--- bin/reduce_bed.R | 2 ++ 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/bin/cdhit_wrapper.R b/bin/cdhit_wrapper.R index 070cb62..ed5ea7f 100644 --- a/bin/cdhit_wrapper.R +++ b/bin/cdhit_wrapper.R @@ -18,8 +18,8 @@ opt <- parse_args(opt_parser) #' cd-hit wrapper #' #' @param input -#' @param similarity cdhit = -c -#' @param coverage In Nucleotides. cdhit = -A +#' @param similarity Similarity threshold. +#' @param coverage Minimal alignment length for both sequences in nucelotides. #' @param output Clustered bedfile. Adds cluster number in last column (lower number = bigger cluster). #' @param clean Clean up after run. #' @@ -42,7 +42,7 @@ cdhitest <- function(input, similarity = 0.8, coverage = 8, output = "cluster.be ### cd-hit-est cdhit_output <- "cdhit_output" - cdhit_call <- paste("cd-hit-est -i", fasta_file, "-o", cdhit_output, "-c", similarity, "-A", coverage, "-G 0 -n 3 -g 1 -r 0 -l 5 -sc 1") + cdhit_call <- paste("cd-hit-est -i", fasta_file, "-o", cdhit_output, "-c", similarity, "-A", coverage, "-G 0 -n 3 -g 1 -r 0 -l 5 -sc 1 -d 0") system(command = cdhit_call, wait = TRUE) diff --git a/bin/reduce_bed.R b/bin/reduce_bed.R index 4590e44..223c946 100644 --- a/bin/reduce_bed.R +++ b/bin/reduce_bed.R @@ -131,6 +131,8 @@ reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", thr #' @param kmer Length of kmer #' @param motif Length of motif #' @param minoverlap Minimum number of bases overlapping between kmer and motif. Must be <= motif & <= kmer. Defaults to ceiling(motif / 2). +#' +#' @return Number of interesting kmer. significant_kmer <- function(bed, kmer, motif, minoverlap = ceiling(motif / 2)) { if (minoverlap > kmer || minoverlap > motif) { stop("Kmer & motif must be greater or equal than minoverlap!")