update function list

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)

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}

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}

man/scaled_pval.Rd

+% 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)
+}
+}

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}