updated readme

R/quantify_edits.R

@@ -9,6 +9,7 @@
 #' @param end_distance_from_cut_site Numeric. The maximum distance from the cut site to consider bases (default: 20).
 #' @param cut_site_start_distance_within_gRNA Numeric. The distance within gRNA to start considering cut sites (default: 3).
 #' @param cut_site_start_distance_outside_gRNA Numeric. The distance outside gRNA to start considering cut sites (default: 3).
+#' @param reference_genome_path Character. Path to a fasta file used to generate the base iGUIDE result (default: '').
 #' @param n_processors Numeric. The number of processors to use for parallel processing (default: 4).
 #' @param overwrite Logical. Whether to overwrite existing analysis output (default: TRUE).
 #'
@@ -26,6 +27,7 @@
 #'   end_distance_from_cut_site = 25,
 #'   cut_site_start_distance_within_gRNA = 4,
 #'   cut_site_start_distance_outside_gRNA = 4,
+#'   reference_genome_path = 'path/to/genome.fasta',
 #'   n_processors = 6,
 #'   overwrite = FALSE
 #' )

README.md

@@ -24,14 +24,15 @@ devtools::install_github('agmcfarland/BEiGUIDE')
 # Running within R
 
 ```R
-quantify_edits(
+BEiGUIDE::quantify_edits(
   base_directory = "path/to/base_directory",
   output_directory = "path/to/output_directory",
   analysis_name = "my_analysis",
   abundance_cutoff = 5,
   end_distance_from_cut_site = 25,
   cut_site_start_distance_within_gRNA = 4,
   cut_site_start_distance_outside_gRNA = 4,
+  reference_genome_path = 'path/to/genome.fasta',
   n_processors = 6,
   overwrite = FALSE
 )
@@ -61,6 +62,9 @@ cut_site_start_distance_within_gRNA:
 cut_site_start_distance_outside_gRNA:
 	Numeric. The distance outside gRNA to start considering cut sites (default: 3).
 
+reference_genome_path
+	Character. Path to a fasta file used to generate the base iGUIDE result (default: '').
+
 n_processors:
 	Numeric. The number of processors to use for parallel processing (default: 4).