From 4dbccb8d3e429f7d847da61cf627875bfda9536a Mon Sep 17 00:00:00 2001
From: Kent Riemondy <kent.riemondy@gmail.com>
Date: Fri, 8 Mar 2024 10:33:32 -0700
Subject: [PATCH] update docs

---
 DESCRIPTION         | 4 ++--
 man/pileup_cells.Rd | 8 +++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1ea8640..e9e82ce 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: raer
 Type: Package
 Title: RNA editing tools in R
-Version: 1.1.3
+Version: 1.1.4
 Authors@R: c(
     person("Kent", "Riemondy", , "kent.riemondy@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0750-1273")),
@@ -63,7 +63,7 @@ SystemRequirements:
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 URL: https://rnabioco.github.io/raer, https://github.com/rnabioco/raer
 BugReports: https://github.com/rnabioco/raer/issues
 biocViews:
diff --git a/man/pileup_cells.Rd b/man/pileup_cells.Rd
index 4964916..fd50674 100644
--- a/man/pileup_cells.Rd
+++ b/man/pileup_cells.Rd
@@ -113,13 +113,18 @@ sce
 
 many_small_bams <- rep(bam_fn, 10)
 bam_ids <- LETTERS[1:10]
+ 
+# for unstranded libraries, sites and alleles should be provided on + strand 
+gr <- GRanges(c("2:579:+", "2:625:+", "2:645:+", "2:589:+", "2:601:+"))
+gr$REF <- c(rep("T", 4), "A")
+gr$ALT <- c(rep("C", 4), "G")
 
 fp <- FilterParam(
     library_type = "unstranded",
     remove_overlaps = TRUE
 )
 
-pileup_cells(many_small_bams,
+sce <- pileup_cells(many_small_bams,
     sites = gr,
     cell_barcodes = bam_ids,
     cb_tag = NULL,
@@ -127,6 +132,7 @@ pileup_cells(many_small_bams,
     outdir,
     param = fp
 )
+sce
 
 unlink(bai)