few minor changes to make it compatible with CRAN

imminfo · Jul 27, 2015 · ca0bf34 · ca0bf34
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diff --git a/R/datatools.R b/R/datatools.R
@@ -1,6 +1,9 @@
 ########## Support functions for managing the data ##########
 
 
+#' Fix alleles - remove allele informatio from columns with genes.
+#' 
+#' @param .data Either tcR data frame or a list with tcR data frames.
 fix.alleles <- function (.data) {
   if (has.class(.data, "list")) {
     lapply(.data, fix.alleles)

diff --git a/R/docdata.R b/R/docdata.R
@@ -52,7 +52,7 @@ AA_TABLE_REVERSED <- AA_TABLE_REVERSED[order(names(AA_TABLE_REVERSED))]
 #' 
 #' @name segments.alphabets
 #' 
-#' @aliases genealphabets HUMAN_TRAV HUMAN_TRAJ HUMAN_TRBV HUMAN_TRBD HUMAN_TRBJ HUMAN_TRBV_MITCR HUMAN_TRGV HUMAN_TRGJ HUMAN_TRDV HUMAN_TRDD HUMAN_TRDJ
+#' @aliases genealphabets HUMAN_TRAV HUMAN_TRAJ HUMAN_TRBV HUMAN_TRBD HUMAN_TRBJ HUMAN_TRBV_MITCR HUMAN_TRGV HUMAN_TRGJ HUMAN_TRDV HUMAN_TRDD HUMAN_TRDJ MOUSE_TRBV MOUSE_TRBJ
 #' 
 #' @usage
 #' HUMAN_TRAV
@@ -126,13 +126,13 @@ HUMAN_TRBV_MITCR <- c('TRBV10-1', 'TRBV10-2', 'TRBV10-3', 'TRBV11-1', 'TRBV11-2'
                       'TRBV5-6', 'TRBV5-8', 'TRBV6-1', 'TRBV6-3, TRBV6-2', 'TRBV6-4', 'TRBV6-5', 'TRBV6-6', 'TRBV6-7',
                       'TRBV7-1', 'TRBV7-2', 'TRBV7-3', 'TRBV7-4', 'TRBV7-6', 'TRBV7-7', 'TRBV7-8', 'TRBV7-9', 'TRBV9')
 
-HUMAN_TRBV_ALS <- c('TRBV10-1', 'TRBV10-2', 'TRBV10-3', 'TRBV11-1', 'TRBV11-2', 'TRBV11-3', 'TRBV12-4', 'TRBV12-3',
-                    'TRBV12-5', 'TRBV13', 'TRBV14', 'TRBV15', 'TRBV16', 'TRBV18', 'TRBV19', 'TRBV2*01',
-                    'TRBV20-1', 'TRBV21-1', 'TRBV23-1', 'TRBV24-1', 'TRBV25-1', 'TRBV27', 'TRBV28', 'TRBV29-1',
-                    'TRBV3-1*01', 'TRBV30', 'TRBV4-1', 'TRBV4-2', 'TRBV4-3', 'TRBV5-1', 'TRBV5-4', 'TRBV5-5',
-                    'TRBV5-6', 'TRBV5-8', 'TRBV6-1', 'TRBV6-3', 'TRBV6-2', 'TRBV6-4', 'TRBV6-5', 'TRBV6-6',
-                    'TRBV6-7', 'TRBV7-1', 'TRBV7-2', 'TRBV7-3', 'TRBV7-4', 'TRBV7-6', 'TRBV7-7', 'TRBV7-8',
-                    'TRBV7-9', 'TRBV9')
+# HUMAN_TRBV_ALS <- c('TRBV10-1', 'TRBV10-2', 'TRBV10-3', 'TRBV11-1', 'TRBV11-2', 'TRBV11-3', 'TRBV12-4', 'TRBV12-3',
+#                     'TRBV12-5', 'TRBV13', 'TRBV14', 'TRBV15', 'TRBV16', 'TRBV18', 'TRBV19', 'TRBV2*01',
+#                     'TRBV20-1', 'TRBV21-1', 'TRBV23-1', 'TRBV24-1', 'TRBV25-1', 'TRBV27', 'TRBV28', 'TRBV29-1',
+#                     'TRBV3-1*01', 'TRBV30', 'TRBV4-1', 'TRBV4-2', 'TRBV4-3', 'TRBV5-1', 'TRBV5-4', 'TRBV5-5',
+#                     'TRBV5-6', 'TRBV5-8', 'TRBV6-1', 'TRBV6-3', 'TRBV6-2', 'TRBV6-4', 'TRBV6-5', 'TRBV6-6',
+#                     'TRBV6-7', 'TRBV7-1', 'TRBV7-2', 'TRBV7-3', 'TRBV7-4', 'TRBV7-6', 'TRBV7-7', 'TRBV7-8',
+#                     'TRBV7-9', 'TRBV9')
 
 
 HUMAN_TRGV <- c()

diff --git a/R/input.R b/R/input.R
@@ -191,7 +191,7 @@ parse.cloneset <- function (.filename,
 
 #' Parse input table files with immune receptor repertoire data.
 #'
-#' @aliases parse.folder parse.file.list parse.file parse.mitcr parse.mitcrbc parse.migec parse.vdjtools parse.immunoseq
+#' @aliases parse.folder parse.file.list parse.file parse.mitcr parse.mitcrbc parse.migec parse.vdjtools parse.immunoseq parse.imseq parse.mixcr
 #'
 #' @description
 #' Load the TCR data from the file with the given filename to a data frame or load all 
@@ -210,13 +210,13 @@ parse.cloneset <- function (.filename,
 #' 
 #' @usage
 #' parse.file(.filename, 
-#' .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...)
+#' .format = c('mitcr', 'mitcrbc', 'migec'), ...)
 #' 
 #' parse.file.list(.filenames, 
-#' .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), .namelist = NA)
+#' .format = c('mitcr', 'mitcrbc', 'migec'), .namelist = NA)
 #' 
 #' parse.folder(.folderpath, 
-#' .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...)
+#' .format = c('mitcr', 'mitcrbc', 'migec'), ...)
 #' 
 #' parse.mitcr(.filename)
 #' 
@@ -288,11 +288,12 @@ parse.cloneset <- function (.filename,
 #' # Parse all files in "~/data/" as MiGEC files.
 #' immdata <- parse.folder("~/data/", 'migec')
 #' }
-parse.folder <- function (.folderpath, .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...) {
+parse.folder <- function (.folderpath, .format = c('mitcr', 'mitcrbc', 'migec'), ...) {
   parse.file.list(list.files(.folderpath, full.names = T), .format)
 }
 
-parse.file.list <- function (.filenames, .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), .namelist = NA) {
+parse.file.list <- function (.filenames, .format = c('mitcr', 'mitcrbc', 'migec'), 
+                             .namelist = NA) {
   # Remove full paths and extension from the given string.
   .remove.ext <- function (.str) {
     gsub(pattern = '.*/|[.].*$', replacement = '', x = .str)
@@ -316,7 +317,7 @@ parse.file.list <- function (.filenames, .format = c('mitcr', 'mitcrbc', 'migec'
   datalist
 }
 
-parse.file <- function(.filename, .format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...) {
+parse.file <- function(.filename, .format = c('mitcr', 'mitcrbc', 'migec'), ...) {
   parse.fun <- switch(.format[1], 
                       mitcr = parse.mitcr,
                       mitcrbc = parse.mitcrbc,
@@ -699,6 +700,7 @@ parse.mixcr <- function (.filename) {
 }
 
 parse.imseq <- function (.filename) {
+  cat("WARNING: I can't understand which chain is it, so you need to modify gene columns in order to use this data frame with tcR.\n")
   f <- gzfile(.filename)
   all.lines <- strsplit(readLines(f), ":", T, useBytes = T)
   close(f)

diff --git a/R/segments.R b/R/segments.R
@@ -162,9 +162,9 @@ geneUsage <- function (.data, .genes = HUMAN_TRBV_MITCR, .quant = c(NA, "read.co
 #' Perform PCA on gene segments frequency data for V- and J-segments and either return pca object or plot the results.
 #' 
 #' @usage
-#' pca.segments(.data, .cast.freq.seg = T, ..., .do.plot = T)
+#' pca.segments(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)
 #' 
-#' pca.segments.2D(.data, .cast.freq.seg = T, ..., .do.plot = T)
+#' pca.segments.2D(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)
 #' 
 #' @param .data Either data.frame or a list of data.frame or a result obtained from the \code{geneUsage} function.
 #' @param .cast.freq.seg if T then apply code{geneUsage} to the supplied data.

diff --git a/data/twa.rda b/data/twa.rda
diff --git a/man/fix.alleles.Rd b/man/fix.alleles.Rd
@@ -0,0 +1,15 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/datatools.R
+\name{fix.alleles}
+\alias{fix.alleles}
+\title{Fix alleles - remove allele informatio from columns with genes.}
+\usage{
+fix.alleles(.data)
+}
+\arguments{
+\item{.data}{Either tcR data frame or a list with tcR data frames.}
+}
+\description{
+Fix alleles - remove allele informatio from columns with genes.
+}
+
diff --git a/man/parse.folder.Rd b/man/parse.folder.Rd
@@ -5,20 +5,22 @@
 \alias{parse.file.list}
 \alias{parse.folder}
 \alias{parse.immunoseq}
+\alias{parse.imseq}
 \alias{parse.migec}
 \alias{parse.mitcr}
 \alias{parse.mitcrbc}
+\alias{parse.mixcr}
 \alias{parse.vdjtools}
 \title{Parse input table files with immune receptor repertoire data.}
 \usage{
 parse.file(.filename,
-.format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...)
+.format = c('mitcr', 'mitcrbc', 'migec'), ...)
 
 parse.file.list(.filenames,
-.format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), .namelist = NA)
+.format = c('mitcr', 'mitcrbc', 'migec'), .namelist = NA)
 
 parse.folder(.folderpath,
-.format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools', 'immunoseq', 'mixcr', 'imseq'), ...)
+.format = c('mitcr', 'mitcrbc', 'migec'), ...)
 
 parse.mitcr(.filename)
 

diff --git a/man/pca.segments.Rd b/man/pca.segments.Rd
@@ -5,9 +5,9 @@
 \alias{pca.segments.2D}
 \title{Perform PCA on segments frequency data.}
 \usage{
-pca.segments(.data, .cast.freq.seg = T, ..., .do.plot = T)
+pca.segments(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)
 
-pca.segments.2D(.data, .cast.freq.seg = T, ..., .do.plot = T)
+pca.segments.2D(.data, .cast.freq.seg = T, ..., .text = T, .do.plot = T)
 }
 \arguments{
 \item{.data}{Either data.frame or a list of data.frame or a result obtained from the \code{geneUsage} function.}

diff --git a/man/segments.alphabets.Rd b/man/segments.alphabets.Rd
@@ -13,6 +13,8 @@
 \alias{HUMAN_TRDV}
 \alias{HUMAN_TRGJ}
 \alias{HUMAN_TRGV}
+\alias{MOUSE_TRBJ}
+\alias{MOUSE_TRBV}
 \alias{genealphabets}
 \alias{segments.alphabets}
 \title{Alphabets of TCR and Ig gene segments.}