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Unverified Commit 6921e84d authored by Laurent Modolo's avatar Laurent Modolo
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update documentation

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Package: criblejurkat
Title: Analysis of FACS data for the Jurkat crible project
Type: Package
Version: 1.0.0
Version: 1.1.0
Authors@R: person("Laurent", "Modolo", email = "laurent.modolo@ens-lyon.fr",
role = c("aut", "cre"))
Description: The package provides a set of function to analyse FCS files.
......@@ -17,9 +17,10 @@ Imports:
flowWorkspace (>= 3.20),
scales (>= 0.5),
Biobase,
biglm,
methods
License: file LICENSE
LazyData: true
Suggests: testthat
RoxygenNote: 6.0.1
RoxygenNote: 6.1.0
BiocViews: CellBasedAssays, FlowCytometry, Software
# Generated by roxygen2: do not edit by hand
export(analysis)
export(anova_lm)
export(anova_rlm)
export(flowset2dataframe)
export(load_annotation)
......@@ -9,11 +10,15 @@ export(plot_column)
export(plot_line)
export(plot_well)
export(project_name)
export(remove_negatives)
export(rm_debris)
export(rm_nonfluo)
export(rm_nonsinglets)
export(set_analysis)
export(split_lm)
import(biglm)
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,exprs)
importFrom(MASS,boxcox)
importFrom(MASS,psi.huber)
importFrom(MASS,rlm)
......@@ -21,12 +26,15 @@ importFrom(flowClust,flowClust)
importFrom(flowClust,getEstimates)
importFrom(flowClust,plot)
importFrom(flowClust,split)
importFrom(flowCore,colnames)
importFrom(flowCore,exprs)
importFrom(flowCore,pData)
importFrom(flowCore,phenoData)
importFrom(flowCore,read.flowSet)
importFrom(flowCore,sampleNames)
importFrom(flowCore,transform)
importFrom(flowCore,transformList)
importFrom(flowCore,truncateTransform)
importFrom(flowWorkspace,GatingSet)
importFrom(flowWorkspace,flowJo_biexp_trans)
importFrom(flowWorkspace,getData)
......
......@@ -121,13 +121,14 @@ batch_effect <- function(data) {
#' @param data a data.frame
#' @param formula (default: "ratio ~ drug + batch") the formula of the model
#' @param lower (default: TRUE) tests if "y" (the ratio) is lower than in controls
#' @param chunk (default: 20000) size of data chunk to do the computation on
#' @param outdir set the outdir directory to a path (default extracted from fcs)
#' @return a data.frame
#' @examples
#' \dontrun{
#' data <- anova_lm(data)
#' }
#' @importFrom biglm
#' @import biglm
#' @importFrom grDevices dev.off pdf
#' @importFrom stats as.formula quantile
#' @export anova_lm
......@@ -154,13 +155,12 @@ anova_lm <- function(data, formula = "ratio ~ drug + batch", lower = TRUE,
#'
#' @param data a data.frame
#' @param formula (default: "ratio ~ drug + batch") the formula of the model
#' @param chunck (default: 200000) chunk size
#' @param chunk (default: 200000) chunk size
#' @return a data.frame
#' @importFrom biglm biglm
#' @import biglm
#' @importFrom stats as.formula quantile
#' @export split_lm
split_lm <- function(data, formula = "ratio ~ drug + batch", chunk = 200000) {
data_index <- seq_len(nrow(data))
data_index <- sample(data_index, nrow(data))
index_start <- 1
......@@ -209,6 +209,7 @@ anova_rlm <- function(data, formula = "ratio ~ drug + batch", lower = TRUE,
return(data)
}
#' @import biglm
#' @importFrom stats pt
compute_pval <- function(model, lower = TRUE) {
model_anova <- data.frame(coef = coef(model),
......
#' remove debris from data
#'
#' @param fcs_data an object of class flowSet
#' @param cluster_number (default: 2) number of cluster to look for
#' @return an object of class flowSet
#' @examples
#' \dontrun{
......
......@@ -38,13 +38,14 @@ set_analysis <- function(data_path = "data/", meta = F) {
#'
#' @param data_path path to folder containing the data sets
#' @param rlm_model (default: TRUE) should rlm model be use or lm ?
#' @param chunk (default: 20000) size of data chunk to do the computation on for lm
#' @return TRUE if everythings ran correclty
#' @examples
#' \dontrun{
#' analysis("data/set_test")
#' }
#' @export analysis
analysis <- function(data_path = "data/", rlm_model = TRUE) {
analysis <- function(data_path = "data/", rlm_model = TRUE, chunk = 20000) {
if (base::file.info(data_path)$isdir) {
set_folders <- list.dirs(data_path, full.names = F)[-1]
} else {
......@@ -102,7 +103,7 @@ analysis <- function(data_path = "data/", rlm_model = TRUE) {
outdir = outdir_rlm)
} else {
data <- anova_lm(data, formula = "ratio ~ drug + batch + set",
outdir = outdir_rlm)
outdir = outdir_rlm, chunk = chunk)
}
for (folder in set_folders) {
message(paste0("plotting for ", folder))
......
......@@ -4,10 +4,14 @@
\alias{analysis}
\title{perform all the analysis for a set of data sets}
\usage{
analysis(data_path = "data/")
analysis(data_path = "data/", rlm_model = TRUE, chunk = 20000)
}
\arguments{
\item{data_path}{path to folder containing the data sets}
\item{rlm_model}{(default: TRUE) should rlm model be use or lm ?}
\item{chunk}{(default: 20000) size of data chunk to do the computation on for lm}
}
\value{
TRUE if everythings ran correclty
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/anova.R
\name{anova_lm}
\alias{anova_lm}
\title{build lm model between drugs accounting for batch effect}
\usage{
anova_lm(data, formula = "ratio ~ drug + batch", lower = TRUE, outdir,
chunk = 20000)
}
\arguments{
\item{data}{a data.frame}
\item{formula}{(default: "ratio ~ drug + batch") the formula of the model}
\item{lower}{(default: TRUE) tests if "y" (the ratio) is lower than in controls}
\item{outdir}{set the outdir directory to a path (default extracted from fcs)}
\item{chunk}{(default: 20000) size of data chunk to do the computation on}
}
\value{
a data.frame
}
\description{
build lm model between drugs accounting for batch effect
}
\examples{
\dontrun{
data <- anova_lm(data)
}
}
......@@ -2,7 +2,7 @@
% Please edit documentation in R/anova.R
\name{anova_rlm}
\alias{anova_rlm}
\title{build rm model between drugs accounting for batch effect}
\title{build rlm model between drugs accounting for batch effect}
\usage{
anova_rlm(data, formula = "ratio ~ drug + batch", lower = TRUE, outdir)
}
......@@ -19,7 +19,7 @@ anova_rlm(data, formula = "ratio ~ drug + batch", lower = TRUE, outdir)
a data.frame
}
\description{
build rm model between drugs accounting for batch effect
build rlm model between drugs accounting for batch effect
}
\examples{
\dontrun{
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/anova.R
\name{split_lm}
\alias{split_lm}
\title{split lm model by chunck with biglm}
\usage{
split_lm(data, formula = "ratio ~ drug + batch", chunk = 2e+05)
}
\arguments{
\item{data}{a data.frame}
\item{formula}{(default: "ratio ~ drug + batch") the formula of the model}
\item{chunk}{(default: 200000) chunk size}
}
\value{
a data.frame
}
\description{
split lm model by chunck with biglm
}
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