From 5a59273d0e9949f37388b46de1b73ae9c70a23cd Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 15 Jul 2022 18:27:37 +0200
Subject: [PATCH] man/*.Rd: update doc
---
man/build_count_matrices.Rd | 18 ++++++++-----
man/cli_run_deseq2.Rd | 2 +-
man/de_analysis.Rd | 13 ++++++++--
man/de_analyzes.Rd | 21 +++++++++++++--
man/filter_dds.Rd | 7 ++---
man/hline.Rd | 19 ++++++++++++++
man/load_matrix.Rd | 7 ++---
man/make_html_pca.Rd | 21 +++++++++++++++
man/make_pca.Rd | 21 +++++++++++++++
man/run_deseq2.Rd | 51 +++++++++++++++++++++++++------------
man/vline.Rd | 19 ++++++++++++++
11 files changed, 166 insertions(+), 33 deletions(-)
create mode 100644 man/hline.Rd
create mode 100644 man/make_html_pca.Rd
create mode 100644 man/make_pca.Rd
create mode 100644 man/vline.Rd
diff --git a/man/build_count_matrices.Rd b/man/build_count_matrices.Rd
index 0f7a019..2b863bb 100644
--- a/man/build_count_matrices.Rd
+++ b/man/build_count_matrices.Rd
@@ -5,28 +5,34 @@
\title{Build matrices}
\usage{
build_count_matrices(
- design,
+ design_table,
path,
- formula,
- filter_file,
+ my_formula,
+ filter_list,
min_expression,
output_folder
)
}
\arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
\item{path}{The path were the count file are stored}
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object}
\item{min_expression}{The minimum average required expression across
all samples to keep the gene}
\item{output_folder}{Folder were the matrices will be produced}
}
+\value{
+The dds object corresponding to a DESeqDatase object obtained after
+running the DESeq function.
+}
\description{
Build matrices
}
diff --git a/man/cli_run_deseq2.Rd b/man/cli_run_deseq2.Rd
index 401056b..8cef804 100644
--- a/man/cli_run_deseq2.Rd
+++ b/man/cli_run_deseq2.Rd
@@ -16,6 +16,6 @@ perform a complete DESeq2 analysis including:
\item Sample loading
\item Normalisation
\item Figure creation
-\item Differential expression analysis for the hcosen contrasts
+\item Differential expression analysis for the chosen contrasts
}
}
diff --git a/man/de_analysis.Rd b/man/de_analysis.Rd
index d978493..fb7e89a 100644
--- a/man/de_analysis.Rd
+++ b/man/de_analysis.Rd
@@ -23,8 +23,17 @@ de_analysis(dds, my_contrast, output_folder, basemean_threshold, lfc_threshold)
\item{basemean_threshold:}{The minimum basemean of gene to be knameept}
}
\value{
-A dataframe indicating The number of differentially expressed genes
-and the number of up and down regulated genes
+A list containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDatase object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
}
\description{
Perform a DESeq2 analysis with a given contrast
diff --git a/man/de_analyzes.Rd b/man/de_analyzes.Rd
index 8cd4162..1facc3f 100644
--- a/man/de_analyzes.Rd
+++ b/man/de_analyzes.Rd
@@ -13,14 +13,31 @@ de_analyzes(
)
}
\arguments{
+\item{dds}{The dds object corresponding to a DESeqDatase object obtained
+after running the DESeq function.}
+
+\item{my_contrasts}{A list containing contrast vectors}
+
\item{output_folder}{Folder where the result table will be created}
\item{lfc_threshold}{The minimum fold change to consider a gene significant}
-\item{my_contrast}{A list containing contrast vectors}
-
\item{basemean_threshold:}{The minimum basemean of genes to be kept}
}
+\value{
+A list containing for each comparison given in my_contrasts
+(keys of the list) a sublist containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDataSet object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
+}
\description{
Perform multiple differential expression analysis
}
diff --git a/man/filter_dds.Rd b/man/filter_dds.Rd
index a3fffce..807c756 100644
--- a/man/filter_dds.Rd
+++ b/man/filter_dds.Rd
@@ -4,19 +4,20 @@
\alias{filter_dds}
\title{Filter DESeq2 object on expressed gene if needed}
\usage{
-filter_dds(dds, filter_file, min_expression, addition_col, formula)
+filter_dds(dds, filter_list, min_expression, addition_col, my_formula)
}
\arguments{
\item{dds}{A dds object}
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object}
\item{min_expression}{The minimum average required expression across all
samples to keep the gene}
\item{addition_col}{Additional design columns}
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
}
\value{
A DESeqDataset object filtered
diff --git a/man/hline.Rd b/man/hline.Rd
new file mode 100644
index 0000000..cecc98c
--- /dev/null
+++ b/man/hline.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/differiential_expression.R
+\name{hline}
+\alias{hline}
+\title{Function to draw a plotly horizontal line}
+\usage{
+hline(y = 0, color = "black")
+}
+\arguments{
+\item{y}{Location of horizontal line}
+
+\item{color}{Color of horizontal line}
+}
+\value{
+a list containing plotly parameters
+}
+\description{
+Function to draw a plotly horizontal line
+}
diff --git a/man/load_matrix.Rd b/man/load_matrix.Rd
index 976867a..59a93f6 100644
--- a/man/load_matrix.Rd
+++ b/man/load_matrix.Rd
@@ -4,14 +4,15 @@
\alias{load_matrix}
\title{Build the deseq2 count matrix from design file}
\usage{
-load_matrix(design, path, formula)
+load_matrix(design_table, path, my_formula)
}
\arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
\item{path}{The path were the count file are stored}
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
}
\value{
A DESeqDataset object filtered
diff --git a/man/make_html_pca.Rd b/man/make_html_pca.Rd
new file mode 100644
index 0000000..44eac28
--- /dev/null
+++ b/man/make_html_pca.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{make_html_pca}
+\alias{make_html_pca}
+\title{Create plotly PCA plot}
+\usage{
+make_html_pca(pca_data, percent_var, output_folder, columns)
+}
+\arguments{
+\item{pca_data}{Object returned by DESeq2::plotPCA containing PCA table}
+
+\item{percent_var}{Vector containing the percentage of variance
+of PC1 and PC2}
+
+\item{output_folder}{Folder where the figure will be created}
+
+\item{columns}{The design columns}
+}
+\description{
+Create plotly PCA plot
+}
diff --git a/man/make_pca.Rd b/man/make_pca.Rd
new file mode 100644
index 0000000..f312f9f
--- /dev/null
+++ b/man/make_pca.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{make_pca}
+\alias{make_pca}
+\title{Make ggplot PCA}
+\usage{
+make_pca(pca_data, percent_var, columns, dds)
+}
+\arguments{
+\item{pca_data}{Object returned by DESeq2::plotPCA containing PCA table}
+
+\item{percent_var}{Vector containing the percentage of variance
+of PC1 and PC2}
+
+\item{columns}{A vector containing the columns to display in PCA data}
+
+\item{dds}{a DESeqDataSet object}
+}
+\description{
+Make ggplot PCA
+}
diff --git a/man/run_deseq2.Rd b/man/run_deseq2.Rd
index e9b18c1..e139a16 100644
--- a/man/run_deseq2.Rd
+++ b/man/run_deseq2.Rd
@@ -5,36 +5,55 @@
\title{DESeq2 wrapper}
\usage{
run_deseq2(
- design,
+ design_table,
path,
- formula,
- filter_file,
- min_expression,
- output_folder,
my_contrasts,
- basemean_threshold,
- lfc_threshold
+ my_formula = "~ condition",
+ filter_list = NULL,
+ min_expression = 2,
+ output_folder = ".",
+ basemean_threshold = 0,
+ lfc_threshold = 0
)
}
\arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
\item{path}{The path were the count file are stored}
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2 (default '~ condition')}
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object, (default NULL)}
\item{min_expression}{The minimum average required expression across
-all samples to keep the gene}
+all samples to keep the gene (default 2)}
-\item{output_folder}{Folder were the matrices will be produced}
+\item{output_folder}{Folder were the matrices will be produced (default .)}
-\item{lfc_threshold}{The minimum fold change to consider a gene significant}
+\item{lfc_threshold}{The minimum fold change to consider a gene significant
+(default 0)}
-\item{my_contrast}{A list containing contrast vectors}
+\item{my_contrast}{A list containing contrast vectors: you can use
+list(c('condition', 'TEST', 'CTRL') to build it)}
-\item{basemean_threshold:}{The minimum basemean of genes to be kept}
+\item{basemean_threshold:}{The minimum basemean of genes to be kept
+(default 0)}
+}
+\value{
+A list containing for each comparison given in my_contrasts
+(keys of the list) a sublist containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDatase object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
}
\description{
DESeq2 wrapper
@@ -45,6 +64,6 @@ perform a complete DESeq2 analysis including:
\item Sample loading
\item Normalisation
\item Figure creation
-\item Differential expression analysis for the hcosen contrasts
+\item Differential expression analysis for the chosen contrasts
}
}
diff --git a/man/vline.Rd b/man/vline.Rd
new file mode 100644
index 0000000..bc6a8ea
--- /dev/null
+++ b/man/vline.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/differiential_expression.R
+\name{vline}
+\alias{vline}
+\title{Function to draw a plotly horizontal line}
+\usage{
+vline(x = 0, color = "black")
+}
+\arguments{
+\item{x}{Location of vertical line}
+
+\item{color}{Color of vertical line}
+}
+\value{
+a list containing plotly parameters
+}
+\description{
+Function to draw a plotly horizontal line
+}
--
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