From 1cbfa730c3a0f22f775b9de7da43aef6db877e6b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 5 Nov 2018 17:26:11 +0100
Subject: [PATCH] update function list
---
NAMESPACE | 2 ++
man/analysis.Rd | 2 +-
man/anova_lm.Rd | 2 +-
man/scaled_pval.Rd | 22 ++++++++++++++++++++++
man/split_lm.Rd | 2 +-
5 files changed, 27 insertions(+), 3 deletions(-)
create mode 100644 man/scaled_pval.Rd
diff --git a/NAMESPACE b/NAMESPACE
index a9a258c..eaf90c3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(remove_negatives)
export(rm_debris)
export(rm_nonfluo)
export(rm_nonsinglets)
+export(scaled_pval)
export(set_analysis)
export(split_lm)
import(biglm)
@@ -59,6 +60,7 @@ importFrom(graphics,par)
importFrom(methods,as)
importFrom(openCyto,add_pop)
importFrom(scales,boxcox_trans)
+importFrom(scales,rescale)
importFrom(stats,as.formula)
importFrom(stats,pt)
importFrom(stats,quantile)
diff --git a/man/analysis.Rd b/man/analysis.Rd
index 95642c0..4f25816 100644
--- a/man/analysis.Rd
+++ b/man/analysis.Rd
@@ -4,7 +4,7 @@
\alias{analysis}
\title{perform all the analysis for a set of data sets}
\usage{
-analysis(data_path = "data/", rlm_model = TRUE, chunk = 20000)
+analysis(data_path = "data/", rlm_model = TRUE)
}
\arguments{
\item{data_path}{path to folder containing the data sets}
diff --git a/man/anova_lm.Rd b/man/anova_lm.Rd
index e1b094a..f2962f2 100644
--- a/man/anova_lm.Rd
+++ b/man/anova_lm.Rd
@@ -5,7 +5,7 @@
\title{build lm model between drugs accounting for batch effect}
\usage{
anova_lm(data, formula = "ratio ~ drug + batch", lower = TRUE, outdir,
- chunk = 20000)
+ chunk = nrow(data))
}
\arguments{
\item{data}{a data.frame}
diff --git a/man/scaled_pval.Rd b/man/scaled_pval.Rd
new file mode 100644
index 0000000..82278c1
--- /dev/null
+++ b/man/scaled_pval.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{scaled_pval}
+\alias{scaled_pval}
+\title{plot the ratio distribution per well}
+\usage{
+scaled_pval(data)
+}
+\arguments{
+\item{data}{data.frame object with a pval column}
+}
+\value{
+data data.frame object with a scaled_pval column
+}
+\description{
+plot the ratio distribution per well
+}
+\examples{
+\dontrun{
+data <- scaled_pval(data)
+}
+}
diff --git a/man/split_lm.Rd b/man/split_lm.Rd
index 5df3fe3..681ef31 100644
--- a/man/split_lm.Rd
+++ b/man/split_lm.Rd
@@ -4,7 +4,7 @@
\alias{split_lm}
\title{split lm model by chunck with biglm}
\usage{
-split_lm(data, formula = "ratio ~ drug + batch", chunk = 2e+05)
+split_lm(data, formula = "ratio ~ drug + batch", chunk = nrow(data))
}
\arguments{
\item{data}{a data.frame}
--
GitLab