From 6ba4ebdf9dbd23dfc606583df04c3f6bfd32c104 Mon Sep 17 00:00:00 2001 From: HDash <16350928+HDash@users.noreply.github.com> Date: Fri, 27 Dec 2024 05:04:38 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20neurogen?= =?UTF-8?q?omics/Power=5FAnalysis=5Fpackage@92b287ec074368ff94bb78b91bd9bf?= =?UTF-8?q?11dc0b9860=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/getting_started.html | 6 +- articles/poweranalysis.html | 6 +- authors.html | 2 +- index.html | 2 +- pkgdown.yml | 4 +- reference/DGE_analysis.html | 4 +- reference/compute_downsampled_corr.html | 2 +- reference/correlation_analysis.html | 144 ++++++++++++++ reference/correlation_boxplots.html | 2 +- reference/differential_expression.html | 2 +- reference/downsampling_DEanalysis.html | 2 +- reference/downsampling_corrplots.html | 2 +- reference/downsampling_range.html | 2 +- reference/index.html | 8 + reference/make_pseudobulk.html | 2 +- reference/plot_celltype_correlation.html | 2 +- reference/plot_de_analysis.html | 2 +- reference/plot_mean_correlation.html | 2 +- reference/power_analysis.html | 2 +- reference/power_plots.html | 2 +- reference/preliminary_plots.html | 2 +- reference/random_permutations.html | 2 +- reference/sample_cells.html | 2 +- reference/sample_individuals.html | 2 +- reference/sex_chromosome_DEGs.html | 2 +- reference/subset_pairs.html | 2 +- ...validate_input_parameters_correlation.html | 184 ++++++++++++++++++ reference/validate_input_parameters_de.html | 2 +- .../validate_input_parameters_power.html | 2 +- reference/within_data_correlation.html | 2 +- sitemap.xml | 2 + 31 files changed, 373 insertions(+), 31 deletions(-) create mode 100644 reference/correlation_analysis.html create mode 100644 reference/validate_input_parameters_correlation.html diff --git a/articles/getting_started.html b/articles/getting_started.html index f986494..c5afb48 100644 --- a/articles/getting_started.html +++ b/articles/getting_started.html @@ -80,7 +80,7 @@

Getting Started

- Source: vignettes/getting_started.Rmd + Source: vignettes/getting_started.Rmd @@ -115,7 +115,9 @@

IntroductionSetup 

-library(poweranalysis)
+library(poweranalysis) +#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : +#> object 'type_sum.accel' not found diff --git a/articles/poweranalysis.html b/articles/poweranalysis.html index 97cf994..5762a9a 100644 --- a/articles/poweranalysis.html +++ b/articles/poweranalysis.html @@ -80,7 +80,7 @@

Power Analysis

- Source: vignettes/poweranalysis.Rmd + Source: vignettes/poweranalysis.Rmd @@ -130,7 +130,9 @@

InstallationSetup 

-library(poweranalysis)
+library(poweranalysis) +#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : +#> object 'type_sum.accel' not found


diff --git a/authors.html b/authors.html index a96deba..5619d39 100644 --- a/authors.html +++ b/authors.html @@ -74,7 +74,7 @@

Authors and Citation

Citation

- Source: DESCRIPTION + Source: DESCRIPTION
diff --git a/index.html b/index.html index 07edfe2..132a865 100644 --- a/index.html +++ b/index.html @@ -82,7 +82,7 @@ Power Analysis
Power Analysis for Differential Expression in scRNA-seq data


R build status
License: MIT + file LICENSE

-

Authors: Salman Fawad, Alan Murphy, Nathan Skene
Updated: Oct-22-2024

+

Authors: Salman Fawad, Alan Murphy, Nathan Skene
Updated: Dec-27-2024

Introduction

diff --git a/pkgdown.yml b/pkgdown.yml index e62efcd..525f772 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ -pandoc: '3.4' +pandoc: 3.6.1 pkgdown: 2.1.1 pkgdown_sha: ~ articles: getting_started: getting_started.html poweranalysis: poweranalysis.html -last_built: 2024-10-22T23:30Z +last_built: 2024-12-27T05:04Z diff --git a/reference/DGE_analysis.html b/reference/DGE_analysis.html index a89f97b..93a2f4e 100644 --- a/reference/DGE_analysis.html +++ b/reference/DGE_analysis.html @@ -54,7 +54,7 @@

Perform differential expression analysis across cell types based on single cell data with Pseudobulk approach. Returns the results of this differential expression analysis

- Source: R/DGE_analysis.R + Source: R/DGE_analysis.R
@@ -178,7 +178,7 @@

Examples

values = genes, mart= mart,useCache = FALSE) gene_IDs <- as.data.table(gene_IDs) setnames(gene_IDs,"ensembl_gene_id","name") -DEGs <- data.table::rbindlist(sc.cell.type.de.return$celltype_DEGs,idcol="celltype") +DEGs <- data.table::rbindlist(sc.cell.type.de.return$celltype_DEGs,idcol="celltype") setkey(DEGs,name) #append gene names DEGs[, gene_name := gene_IDs[DEGs, on=.(name), x.hgnc_symbol]] diff --git a/reference/compute_downsampled_corr.html b/reference/compute_downsampled_corr.html index a0738b2..41196d0 100644 --- a/reference/compute_downsampled_corr.html +++ b/reference/compute_downsampled_corr.html @@ -54,7 +54,7 @@

For a given down-sampled DE output, computes the correlation of the log-foldchange of the DEGs (at specified p-value) for a given dataset (celltype)

- Source: R/compute_downsampled_corr.r + Source: R/compute_downsampled_corr.r
diff --git a/reference/correlation_analysis.html b/reference/correlation_analysis.html new file mode 100644 index 0000000..5b3d769 --- /dev/null +++ b/reference/correlation_analysis.html @@ -0,0 +1,144 @@ + +Runs correlation analysis pipeline — correlation_analysis • poweranalysis + + +
+
+ + + +
+
+
+

Runs correlation analysis pipeline

+ Source: R/correlation_analysis.r + +
+ +
+

Runs correlation analysis pipeline

+
+ +
+ 
correlation_analysis(
+  dataset_name = "placeholder",
+  allstudies = "placeholder",
+  celltypes = "placeholder",
+  pvals = c(0.05, 0.025, 0.01, 0.001, 1e-04),
+  data_names = "placeholder",
+  alphaval = "placeholder",
+  numPerms = "placeholder",
+  numSubsets = "placeholder",
+  output_path = getwd()
+)
+
+ +
+

Arguments

+ + +
dataset_name
+

name of the dataset used to select significant DEGs from (specified as a string, name as in allstudies)

+ + +
allstudies
+

a list containing all the datasets (as SCE objects)

+ + +
celltypes
+

a list containing the celltypes to compute mean correlation across

+ + +
pvals
+

list of p-value cut-offs which will be used to select DEGs

+ + +
data_names
+

names of the datasets as they appear in the correlation plot

+ + +
alphaval
+

(alpha) transparency of the non-mean boxplots

+ + +
numPerms
+

number of random permutations of the dataset used to select significant DEGs from

+ + +
numSubsets
+

number of pairs of random subsets of the dataset used to select significant DEGs from

+ + +
output_path
+

base path in which outputs will be stored +Saves all plots and DE outputs in the appropriate directories

+ +
+ +
+ +
+ + +
+

Developed by Salman Fawad, Yunning Yuan.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/correlation_boxplots.html b/reference/correlation_boxplots.html index 20b286c..3ccc754 100644 --- a/reference/correlation_boxplots.html +++ b/reference/correlation_boxplots.html @@ -54,7 +54,7 @@

Obtain box plots for the correlations of all celltypes, and the mean correlations at a specified cutoff p-value

- Source: R/correlation_boxplots.r + Source: R/correlation_boxplots.r
diff --git a/reference/differential_expression.html b/reference/differential_expression.html index cfc80da..60c3933 100644 --- a/reference/differential_expression.html +++ b/reference/differential_expression.html @@ -54,7 +54,7 @@

Differential Expression Analysis using edgeR LRT on pseudobulk data

- Source: R/differential_expression.R + Source: R/differential_expression.R
diff --git a/reference/downsampling_DEanalysis.html b/reference/downsampling_DEanalysis.html index 14c1ebc..ae5fae8 100644 --- a/reference/downsampling_DEanalysis.html +++ b/reference/downsampling_DEanalysis.html @@ -54,7 +54,7 @@

Downsample the dataset, based either on the individuals or cells, and run DE analysis on each downsampled output. Save results in a dataframe

- Source: R/downsampling_DEanalysis.r + Source: R/downsampling_DEanalysis.r
diff --git a/reference/downsampling_corrplots.html b/reference/downsampling_corrplots.html index 884dfb5..76fcd4a 100644 --- a/reference/downsampling_corrplots.html +++ b/reference/downsampling_corrplots.html @@ -54,7 +54,7 @@

Create correlation plots of the effect sizes of the top 1000 and top 500 DEGs

- Source: R/downsampling_corrplots.r + Source: R/downsampling_corrplots.r
diff --git a/reference/downsampling_range.html b/reference/downsampling_range.html index 6f4bb60..37e1a2a 100644 --- a/reference/downsampling_range.html +++ b/reference/downsampling_range.html @@ -54,7 +54,7 @@

Obtain the range of values to downsample at (either for individuals, or mean number of cells per individual)

- Source: R/downsampling_range.r + Source: R/downsampling_range.r
diff --git a/reference/index.html b/reference/index.html index 1994b51..f281d1f 100644 --- a/reference/index.html +++ b/reference/index.html @@ -68,6 +68,10 @@

All functions compute_downsampled_corr()

For a given down-sampled DE output, computes the correlation of the log-foldchange of the DEGs (at specified p-value) for a given dataset (celltype)

+ +

correlation_analysis()

+ +

Runs correlation analysis pipeline

correlation_boxplots()

@@ -136,6 +140,10 @@

All functions subset_pairs()

Obtain independent pairs of subsets of a specified dataset, based on sample ID

+ +

validate_input_parameters_correlation()

+ +

Tests input parameters for functions

validate_input_parameters_de()

diff --git a/reference/make_pseudobulk.html b/reference/make_pseudobulk.html index 267ed84..64d8506 100644 --- a/reference/make_pseudobulk.html +++ b/reference/make_pseudobulk.html @@ -54,7 +54,7 @@

Calculate the summed pseudobulk values for an SCE object based on one single cell type only. Ensure to filter SCE to pass one cell type's data.

- Source: R/make_pseudobulk.R + Source: R/make_pseudobulk.R
diff --git a/reference/plot_celltype_correlation.html b/reference/plot_celltype_correlation.html index 38fbd6d..8012a91 100644 --- a/reference/plot_celltype_correlation.html +++ b/reference/plot_celltype_correlation.html @@ -54,7 +54,7 @@

Computes the correlation of the log-foldchange of the DEGs (at specified p-value) for a given celltype, across all datasets

- Source: R/plot_celltype_correlation.r + Source: R/plot_celltype_correlation.r
diff --git a/reference/plot_de_analysis.html b/reference/plot_de_analysis.html index e657379..b6eb4ea 100644 --- a/reference/plot_de_analysis.html +++ b/reference/plot_de_analysis.html @@ -54,7 +54,7 @@

Create differential expression analysis plots. Run by DGE_analysis()

- Source: R/plot_de_analysis.R + Source: R/plot_de_analysis.R
diff --git a/reference/plot_mean_correlation.html b/reference/plot_mean_correlation.html index ff8a7b7..853a81e 100644 --- a/reference/plot_mean_correlation.html +++ b/reference/plot_mean_correlation.html @@ -54,7 +54,7 @@

Obtain the average correlation (across celltypes) at a specified cutoff p-value

- Source: R/plot_mean_correlation.r + Source: R/plot_mean_correlation.r
diff --git a/reference/power_analysis.html b/reference/power_analysis.html index 4ca6447..64e5757 100644 --- a/reference/power_analysis.html +++ b/reference/power_analysis.html @@ -54,7 +54,7 @@

Runs entire power analysis pipeline

- Source: R/power_analysis.r + Source: R/power_analysis.r
diff --git a/reference/power_plots.html b/reference/power_plots.html index 8237764..a69315e 100644 --- a/reference/power_plots.html +++ b/reference/power_plots.html @@ -54,7 +54,7 @@

Create plots for power analysis, with down-sampling based either on the individuals or cells

- Source: R/power_plots.r + Source: R/power_plots.r
diff --git a/reference/preliminary_plots.html b/reference/preliminary_plots.html index 8311b2b..82c8421 100644 --- a/reference/preliminary_plots.html +++ b/reference/preliminary_plots.html @@ -54,7 +54,7 @@

Create preliminary plots for data exploration

- Source: R/preliminary_plots.r + Source: R/preliminary_plots.r
diff --git a/reference/random_permutations.html b/reference/random_permutations.html index a2234c7..a37d7fb 100644 --- a/reference/random_permutations.html +++ b/reference/random_permutations.html @@ -54,7 +54,7 @@

Obtain highly randomised permutations of a specified dataset (based on sex labels), while maintaining consistency with the sample ID

- Source: R/random_permutations.r + Source: R/random_permutations.r
diff --git a/reference/sample_cells.html b/reference/sample_cells.html index 3ade819..05b9bdf 100644 --- a/reference/sample_cells.html +++ b/reference/sample_cells.html @@ -54,7 +54,7 @@

Sample the data for a specified mean number of cells (per sample) from the dataset

- Source: R/sample_cells.r + Source: R/sample_cells.r
diff --git a/reference/sample_individuals.html b/reference/sample_individuals.html index 77d3606..2b09157 100644 --- a/reference/sample_individuals.html +++ b/reference/sample_individuals.html @@ -54,7 +54,7 @@

Sample the data for a specified number of individuals from the dataset

- Source: R/sample_individuals.r + Source: R/sample_individuals.r
diff --git a/reference/sex_chromosome_DEGs.html b/reference/sex_chromosome_DEGs.html index 4d692bc..331b6dc 100644 --- a/reference/sex_chromosome_DEGs.html +++ b/reference/sex_chromosome_DEGs.html @@ -54,7 +54,7 @@

Given a DGE analysis output, this outputs a subset of the analysis with the genes laying only on the sex chromosomes (X/Y)

- Source: R/sex_chromosome_DEGs.r + Source: R/sex_chromosome_DEGs.r
diff --git a/reference/subset_pairs.html b/reference/subset_pairs.html index 30dd761..08a9d0e 100644 --- a/reference/subset_pairs.html +++ b/reference/subset_pairs.html @@ -54,7 +54,7 @@

Obtain independent pairs of subsets of a specified dataset, based on sample ID

- Source: R/subset_pairs.r + Source: R/subset_pairs.r
diff --git a/reference/validate_input_parameters_correlation.html b/reference/validate_input_parameters_correlation.html new file mode 100644 index 0000000..feefa5b --- /dev/null +++ b/reference/validate_input_parameters_correlation.html @@ -0,0 +1,184 @@ + +Tests input parameters for functions — validate_input_parameters_correlation • poweranalysis + + +
+
+ + + +
+
+
+

Tests input parameters for functions

+ Source: R/validate_input_parameters_correlation.r + +
+ +
+

Tests input parameters for functions

+
+ +
+ 
validate_input_parameters_correlation(
+  dataset_name = "placeholder",
+  allstudies = "placeholder",
+  celltypes = "placeholder",
+  pvalue = "placeholder",
+  data_names = "placeholder",
+  corrMats = "placeholder",
+  numRealDatasets = "placeholder",
+  alphaval = "placeholder",
+  numPerms = "placeholder",
+  numSubsets = "placeholder",
+  sexDEGs = "placeholder",
+  fontsize_yaxislabels = "placeholder",
+  fontsize_yaxisticks = "placeholder",
+  fontsize_title = "placeholder",
+  fontsize_legendlabels = "placeholder",
+  fontsize_legendtitle = "placeholder",
+  fontsize_facet_labels = "placeholder"
+)
+
+ +
+

Arguments

+ + +
dataset_name
+

name of the dataset used to select significant DEGs from (specified as a string, name as in allStudies)

+ + +
allstudies
+

a list containing all the datasets (most likely as SCE objects)

+ + +
celltypes
+

a list containing the celltypes to compute mean correlation across

+ + +
pvalue
+

the cut-off p-value which will be used to select DEGs

+ + +
data_names
+

names of the datasets as they appear in the correlation plot

+ + +
corrMats
+

(named) list of correlation matrices for each celltype with the final element being the mean correlation matrix, all at specified p-value

+ + +
numRealDatasets
+

total number of real datasets (most likely the number of studies, but sometimes a study may be split e.g. into 2 brain regions, so in this case it would be the number of studies plus 1)

+ + +
alphaval
+

(alpha) transparency of the non-mean boxplots

+ + +
numPerms
+

number of random permutations of the dataset used to select significant DEGs from

+ + +
numSubsets
+

number of pairs of random subsets of the dataset used to select significant DEGs from

+ + +
sexDEGs
+

true if DEGs come from sex chromosomes, else false

+ + +
fontsize_yaxislabels
+

font size for axis labels in plot

+ + +
fontsize_yaxisticks
+

font size for axis tick labels in plot

+ + +
fontsize_title
+

font size for plot title

+ + +
fontsize_legendlabels
+

font size for legend labels in plot

+ + +
fontsize_legendtitle
+

font size for legend title in plot

+ + +
fontsize_facet_labels
+

font size for facet labels +Checks all correlation analysis parameters are specified correctly

+ +
+ +
+ +
+ + +
+

Developed by Salman Fawad, Yunning Yuan.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/validate_input_parameters_de.html b/reference/validate_input_parameters_de.html index a5033c3..fcaca31 100644 --- a/reference/validate_input_parameters_de.html +++ b/reference/validate_input_parameters_de.html @@ -54,7 +54,7 @@

Validate that there are no user input errors for the differential expression analysis - sc.cell.type.de

- Source: R/validate_input_parameters_de.R + Source: R/validate_input_parameters_de.R
diff --git a/reference/validate_input_parameters_power.html b/reference/validate_input_parameters_power.html index dcd9c05..af0c168 100644 --- a/reference/validate_input_parameters_power.html +++ b/reference/validate_input_parameters_power.html @@ -54,7 +54,7 @@

Tests input parameters for functions

- Source: R/validate_input_parameters_power.r + Source: R/validate_input_parameters_power.r
diff --git a/reference/within_data_correlation.html b/reference/within_data_correlation.html index f99ef76..1cfbbea 100644 --- a/reference/within_data_correlation.html +++ b/reference/within_data_correlation.html @@ -54,7 +54,7 @@

Create correlation plots of the effect sizes, between random permutations and subsets of a given dataset

- Source: R/within_data_correlation.r + Source: R/within_data_correlation.r
diff --git a/sitemap.xml b/sitemap.xml index d880cd4..82ce65c 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -9,6 +9,7 @@ /index.html /reference/DGE_analysis.html /reference/compute_downsampled_corr.html +/reference/correlation_analysis.html /reference/correlation_boxplots.html /reference/differential_expression.html /reference/downsampling_DEanalysis.html @@ -27,6 +28,7 @@ /reference/sample_individuals.html /reference/sex_chromosome_DEGs.html /reference/subset_pairs.html +/reference/validate_input_parameters_correlation.html /reference/validate_input_parameters_de.html /reference/validate_input_parameters_power.html /reference/within_data_correlation.html