From dedb472d231b540cc1907fe13cd6cc87aff23091 Mon Sep 17 00:00:00 2001
From: jcalendo <jcalendo@gmail.com>
Date: Tue, 15 Oct 2024 15:46:12 -0400
Subject: [PATCH] Add normalized avg by default

---
 R/{pileup_profile.R => pileup-profile.R} | 11 +++++------
 man/dot-pileup2dt.Rd                     |  2 +-
 man/pileup_profile.Rd                    |  2 +-
 3 files changed, 7 insertions(+), 8 deletions(-)
 rename R/{pileup_profile.R => pileup-profile.R} (93%)

diff --git a/R/pileup_profile.R b/R/pileup-profile.R
similarity index 93%
rename from R/pileup_profile.R
rename to R/pileup-profile.R
index 31c64e3..d0ed5d1 100644
--- a/R/pileup_profile.R
+++ b/R/pileup-profile.R
@@ -79,12 +79,10 @@ pileup_profile <- function(bamfile, x, scan_bam_flag, sample_size = NULL,
 
   if (!is.null(sample_size)) {
     n <- floor(sample_size / 2)
-    
     if (n > length(pos_gr) || n > length(neg_gr)) {
       n <- min(c(length(pos_gr), length(neg_gr)))
       message("subsample size > length of ranges on either strand. Setting n to ", n)
     }
-    
     pos_gr <- pos_gr[sample.int(length(pos_gr), size = n)]
     neg_gr <- neg_gr[sample.int(length(neg_gr), size = n)]
   }
@@ -96,12 +94,13 @@ pileup_profile <- function(bamfile, x, scan_bam_flag, sample_size = NULL,
   np <- .pileup2dt(Rsamtools::pileup(bamfile, scanBamParam = neg_bparam, pileupParam = pparam))
   
   # Start counting from the 5' end
-  pp[, RelativePosition := pos - start]
-  np[, RelativePosition := end - pos]
+  pp[, relative_position := pos - start]
+  np[, relative_position := end - pos]
   df <- rbind(pp, np)
 
-  result <- df[, .(Sum = sum(count), Avg = mean(count), N = .N), by = RelativePosition]
-  data.table::setorder(result, RelativePosition)
+  result <- df[, .(n = .N, total = sum(count), avg = mean(count)), by = relative_position]
+  result[, normalized := coriell::minmax(avg)]
+  data.table::setorder(result, relative_position)
 
   return(result)
 }
diff --git a/man/dot-pileup2dt.Rd b/man/dot-pileup2dt.Rd
index 356ed13..fe6a144 100644
--- a/man/dot-pileup2dt.Rd
+++ b/man/dot-pileup2dt.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pileup_profile.R
+% Please edit documentation in R/pileup-profile.R
 \name{.pileup2dt}
 \alias{.pileup2dt}
 \title{Convert pileups to data.tables}
diff --git a/man/pileup_profile.Rd b/man/pileup_profile.Rd
index 0e56118..2d140c1 100644
--- a/man/pileup_profile.Rd
+++ b/man/pileup_profile.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pileup_profile.R
+% Please edit documentation in R/pileup-profile.R
 \name{pileup_profile}
 \alias{pileup_profile}
 \title{Return the pileup of reads over a set of GRanges}