Added documentation

Author: siddiquiz

R/Rchimerism.R

@@ -1,6 +1,13 @@
 
 
 #' Rchimerism
+#'
+#' Use Rchimerism through the shiny interface
+#'
+#' This function allows the user to input data files
+#' and view the chimerism percentages along with the input data matrices
+#' through the browser interface, with the options to download the results
+#'
 #' @name Rchimerism
 #' @importFrom shiny fluidPage
 #' @importFrom shiny titlePanel
@@ -27,6 +34,8 @@
 #' @importFrom shiny stopApp
 #' @importFrom shiny shinyApp
 #' @importFrom shiny shinyUI
+#'
+#' @return Returns nothing
 
 #' @export
 

R/chiDD.R

@@ -1,9 +1,16 @@
-##############################################################
-# Double Donor
-# Based on the informative alleles, calculate donor proportion
-# Input: rcode.profile; rcode.markers; sdata.txt
-# Output: results.xls
-##############################################################
+
+#' Rchimerism chiDD
+#'
+#' An internal function to determine donor percentages for a single donor
+#'
+#'
+#' @param sdata Sample data input text file
+#' @param markers List of locus markers
+#' @param profile,ru,rt,rnn,d1nn,d2nn,d1u,d2u,d1t,d2t,r Internal variables for matrix operations
+#'
+#' @return A data frame with donor percentage results, and sample allele matrix
+#'
+#'
 
 
 #load('locusDD.RData'); #load the previous workplace (r, d, markers, profile)

R/chiSD.R

@@ -1,9 +1,17 @@
-##############################################################
-# Single Donor
-# Based on the informative alleles, calculate donor proportion
-# Input: rcode.profile; rcode.markers; sdata.txt
-# Output: results.xls
-##############################################################
+
+#' Rchimerism chiSD
+#'
+#' An internal function to determine donor percentages for a single donor
+#'
+#'
+#' @param sdata Sample data input text file
+#' @param markers List of locus markers
+#' @param profile,rt,dt,d,r Internal variables for matrix operations
+#'
+#' @return A data frame with donor percentage results, and sample allele matrix
+#'
+#'
+
 
 
 #sdata,markers,rt,dm,rm

R/locDD.R

@@ -1,8 +1,22 @@
+
+
+#' Rchimerism locDD
+#'
+#' An internal function to determine informative loci for double donor cases
+#'
+#'
+#' @param donor1_data Donor 1 data input text file
+#' @param donor2_data Donor 2 data input text file
+#' @param recipient_data Recipient data input text file
+#' @param markers List of locus markers
+#'
+#'
+#' @return Internal variables used by chiDD.R
+
+# Output: profile,ru,rt,rnn,d1nn,d2nn,d1u,d2u,d1t,d2t,r,d1m,d2m,rm
 #############################################
-# Decide informative loci for double donor
-# Input: ddata.txt; rdata.txt
-# Output: rcode.profile; rcode.markers; rcode.donor; rcode.recipient;
-#############################################
+
+
 
 #markers = c('D3S1358','TH01','D21S11','D18S51','Penta E','D5S818','D13S317','D7S820','D16S539','CSF1PO','Penta D','vWA','D8S1179','TPOX','FGA');
 locDD <- function(donor1_data, donor2_data,recipient_data,markers) {

R/locSD.R

@@ -1,10 +1,15 @@
-#############################################
-# Decide informative loci for single donor
-# Input: ddata.txt; rdata.txt
-# Output: rcode.profile; rcode.markers; rcode.donor; rcode.recipient;
-#############################################
 
 
+#' Rchimerism locSD
+#'
+#' An internal function to determine informative loci for a single donor
+#'
+#'
+#' @param ddata Donor data input text file
+#' @param rdata Recipient data input text file
+#' @param markers List of locus markers
+#'
+#' @return Internal variables used by chiSD.R
 
 locSD <- function(ddata,rdata,markers) {
 #markers = c('D3S1358','TH01','D21S11','D18S51','Penta E','D5S818','D13S317','D7S820','D16S539','CSF1PO','Penta D','vWA','D8S1179','TPOX','FGA');