From 3d343f4e4c8668123d90460f93885c89b459bc43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A1rbara=20Bitarello?= <barbarabitarello@gmail.com>
Date: Fri, 19 Apr 2024 19:19:22 -0400
Subject: [PATCH] Update ncd1.Rd

---
 man/ncd1.Rd | 66 +++++++----------------------------------------------
 1 file changed, 8 insertions(+), 58 deletions(-)

diff --git a/man/ncd1.Rd b/man/ncd1.Rd
index 653ffc52..6702d4a2 100644
--- a/man/ncd1.Rd
+++ b/man/ncd1.Rd
@@ -4,81 +4,31 @@
 \alias{ncd1}
 \title{Calculate non-central statistic (NCD1)}
 \usage{
-ncd1(
-  x = x,
-  tf = 0.5,
-  fold = T,
-  w = 3000,
-  by.snp = TRUE,
-  mid = FALSE,
-  ncores = 2,
-  selectwin = "val",
-  targetpos = NULL,
-  minIS = 2,
-  label = NULL,
-  verbose = T
-)
-
-ncd1(
-  x = x,
-  tf = 0.5,
-  fold = T,
-  w = 3000,
-  by.snp = TRUE,
-  mid = FALSE,
-  ncores = 2,
-  selectwin = "val",
-  targetpos = NULL,
-  minIS = 2,
-  label = NULL,
-  verbose = T
-)
+ncd1(x = x, tf = 0.5, w = 3000, ncores = 2, minIS = 2, by = "POS")
 }
 \arguments{
-\item{x}{A data.table object}
-
-\item{tf}{Target frequency}
-
-\item{fold}{Logical. If TRUE, NCD1 will use minor allele frequencies.}
-
-\item{w}{Window size in bp. Default is 1000}
-
-\item{by.snp}{Logical. If TRUE, windows are defined around each SNP
-in the input data. Else, slidding windows in the range first pos:last pos
-will be used.}
-
-\item{mid}{Logical. If TRUE runs NCD centered on a core SNP frequency instead of a pre-defined tf. Requires targetpos.}
+\item{x}{A data.table object with
+columns: CHR, POS, REF, ALT, tx_1 (number of alternate allele copies),
+tn_1 (total number of alleles).}
 
-\item{ncores}{Number of cores. Increasing this can spead things up for you.
-Default is 4.}
+\item{tf}{Target frequency.}
 
-\item{selectwin}{Select window. "val" returns the window with the lowest test. "maf" returns the window
-which has the lowest difference between its central MAF and the tf."mid" returns the window
-centered closest on a value provided by the user under targetpos."all" returns all windows (idea for when the user wants to select windows after scanning a genome)}
+\item{w}{Window size in bp. Default is 3000.}
 
-\item{targetpos}{Position of the target SNP. Only needed for mid==T}
+\item{ncores}{Number of cores. Increasing this can speed things up for you.
+Default is 2.}
 
 \item{minIS}{Minimum number of informative sites. Default is 2. Windows with
 less informative sites than this threshold are discarded.}
 
-\item{label}{An optional label to include as the last column of the output. Defaults to value in selectwin.}
-
-\item{verbose}{Logical. If TRUE, progress reports will be printed as the
-function runs.}
-
 \item{by}{Define how to scan the genome. "POS" (default) defined sliding windows based on w. "IS" defined windows around each informative site.}
 }
 \value{
 A data.table object with columns:  Win.ID, S (sites), IS (informative sites), tf, ncd1
-
-A data.table object
 }
 \description{
-Calculate non-central statistic (NCD1)
-
 Calculate non-central statistic (NCD1)
 }
 \examples{
 ncd1(x=ncd1_input, tf=0.5, w=3000, ncores=2, minIS=8)
-ncd1(x=ncd1_input, selectwin="mid", targetpos=15000, mid=TRUE)
 }