Man pages for LUMC/DGE_analysis
dgeAnalysis

addAnnotationsFromTableToSEAdd annotation to the SummerizedExperiment.
addSamplesFromTableToSEAdd samples to the SummerizedExperiment.
alignment_summaryPrepare data for alignment plot
barcodePrepare data for barcode plot
barcode_plotCreate barcode plot with ggplot2
bar_plotCreate bar plot with ggplot2
bias_gcPrepare data for GC bias plot
cnet_dataPrepare data for concept network plot
cnetPlotlyGenes are gathered from enrichment result from specific...
complexityPrepare data for complexity plot
complexityDataCreates dataframe with number of reads per gene, ordered on...
count_distPrepare data for count distribution plot
createContrastCreate contrast by finding matrix values in the design...
createDesignCreate vector from two design values and two matrix values....
createMatrixGetbase column and use this to create right matrix. Loop...
dendro_dataPrepare data for dendrogram plot
dendro_plotCreate dendrogram plot with ggplot2
de_ratioPrepare data for expression ratio plot
enrich_barPrepare data for enriched bar plot
enrich_barDEPrepare data for enriched bar plot with DE genes
extract_geneSetsCollect genes within a pathway. Gets genes from enrichment...
fix_violin_hoverFix hover info for violin plot, as it cant find CPM values
gene_strandPrepare data for gene strand bias plot
getCountCount the read counts per feature to find number of reads...
get_dendrogram_dataGet heigth information from tree object. Get labels/names...
get_organismIDThe gene IDs are gathered from DE table. The first part of...
heat_dePrepare data for heatmap plot
heatmap_plotCreate heatmap plot with ggplot2
heat_varPrepare data for heatmap plot
informationBoxTemplate for plot information.
line_plotCreate line plot with ggplot2
list2dfThe inputList is converted to a dataframe format. Dataframe...
list2graphThe inputList is converted to a dataframe. The dataframe is...
maPrepare data for MA plot
mds_clustPrepare data for MDS plot
network_plotCreate network plot with ggplot2
pca_dataPrepare data for PCA plot
pvalue_dataPrepare data for pvalue plot
readCountsFromTableAdd all counts that are in samples in SummerizedExperiment.
relevelSamplesCreate vector from two matrix values. Try to relevel samples...
scatter_plotCreate scatter plot with ggplot2
stackDgeStacks total DGE counts based on: mapping feature (aligned,...
startAppStart dgeAnalysis application.
tsne_dataPrepare data for tSNE plot
violin_distPrepare data for violin distribution plot
violin_plotCreate violin plot with ggplot2
volcanoPrepare data for volcano plot
voom_dataPrepare data for voom plot
LUMC/DGE_analysis documentation built on Aug. 12, 2022, 11:04 p.m.