From d570e25ec1645444d3d3b187954b856eab8c1480 Mon Sep 17 00:00:00 2001
From: Geo Pertea <geo.pertea@gmail.com>
Date: Sat, 21 Sep 2024 21:10:14 -0400
Subject: [PATCH] cleanup comments from vignette, add the new functions

---
 man/normalize_tx_names.Rd | 21 +++++++++++++++++++++
 man/which_tx_names.Rd     | 25 +++++++++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 man/normalize_tx_names.Rd
 create mode 100644 man/which_tx_names.Rd

diff --git a/man/normalize_tx_names.Rd b/man/normalize_tx_names.Rd
new file mode 100644
index 0000000..5e4174b
--- /dev/null
+++ b/man/normalize_tx_names.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{normalize_tx_names}
+\alias{normalize_tx_names}
+\title{Remove version number from Gencode/Ensembl transcript names}
+\usage{
+normalize_tx_names(txnames)
+}
+\arguments{
+\item{txnames}{A \code{character()} vector of GENCODE or ENSEMBL transcript IDs}
+}
+\value{
+A
+\code{character()} vector of transcript names without versioning
+}
+\description{
+This function removes the Gencode/ENSEMBL version from the transcript ID, while protecting _PAR_Y suffixes if present
+}
+\examples{
+ensIDs <-  normalize_tx_names(rownames(rse_tx))
+}
diff --git a/man/which_tx_names.Rd b/man/which_tx_names.Rd
new file mode 100644
index 0000000..f57a173
--- /dev/null
+++ b/man/which_tx_names.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{which_tx_names}
+\alias{which_tx_names}
+\title{Check validity of transcript vectors and return a vector matching indexes in tx1}
+\usage{
+which_tx_names(txnames, sig_transcripts)
+}
+\arguments{
+\item{tx1}{A \code{character()} vector of GENCODE or ENSEMBL transcript IDs.}
+
+\item{tx2}{A \code{character()} vector of GENCODE or ENSEMBL transcript IDs.}
+}
+\value{
+A
+\code{integer()} vector of \code{tx1} transcript indexes in \code{tx2}.
+}
+\description{
+This function is used to check if tx1 and tx2 are GENCODE or ENSEMBL transcript IDs
+and return an integer vector of tx1 transcript indexes that are in tx2.
+}
+\examples{
+sig_tx <-  select_transcripts("cell_component")
+whichTx <- which_tx_names(rownames(rse_tx), sig_tx)
+}