updated

README.md

@@ -33,9 +33,10 @@ Three files are obtained using the Axiom genotyping pipeline:
 
 To read these files, use the following commands:
 
-`axiom_calls <- readr::read_tsv(path_to_axiom_calls_file)`
+`axiom_calls <- readr::read_tsv(path_to_axiom_calls_file)`  
 `axiom_confidences <- svsniper::read_confidences(path_to_axiom_confidences_file)`  
-`axiom_summary <- svsniper::read_summary(path_to_axiom_summary_file)`
+`axiom_summary <- svsniper::read_summary(path_to_axiom_summary_file)`  
+
 
 **Optional step: filter SNPs**
 
@@ -43,6 +44,14 @@ You may want to remove SNPs with bad confidence scores, and/or, depending on
 the type of analysis you want to run, SNPs with high minor allele frequencies.  
 In order to filter out SNPs, three functions are available:
 
+`svsniper::count_confidences(axiom_confidences, threshold = 0.15`
+This function will count the number of samples with a confidence score above the
+defined threshold (defaults to 0.15, the value used in the Affymetrix Axiom 
+tools), and returns a table as shown below:  
+
+
+
+
 `svsniper::count_alleles(axiom_calls)`  
 
 This function will return a table as shown below: