wrapDESeq2: Differential expression analysis with DESeq2

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Differential Gene expression analysis for multiple group comparisons incl. output of Venn diagrams, volcano plots and heatmaps.

Usage

wrapDESeq2(
  dds,
  comparisons,
  min_rowsum = 10,
  p_value_threshold = 0.05,
  adjust.method = "BH",
  fc_threshold = log2(1.5),
  projectfolder = file.path("GEX/deseq"),
  projectname = "",
  symbolColumn = NULL,
  sampleColumn = "Sample_Name",
  groupColumn = "Sample_Group",
  add_anno_columns = NULL,
  venn_comparisons = NULL,
  maxHM = 50,
  scale = c("none"),
  HMcexRow = 1.1,
  HMcexCol = 1.1,
  figure.res = 300,
  HMincludeRelevantSamplesOnly = TRUE,
  color.palette = "heat.colors"
)

Arguments

dds	DESeqDataSet
comparisons	character vector with group comparisons in format "groupA-groupB"
min_rowsum	numeric. Minimum rowsum of countmatrix of dds. All rows with rowSums < min_rowsum are removed from the count matrix.
p_value_threshold	numeric p-value threshold
adjust.method	adjustment method for multiple testing ("none", "BH", "BY" and "holm")
fc_threshold	numeric foldchange threshold on logarithmic scale to base 2.
projectfolder	character with directory for output files (will be generated if not exisiting).
projectname	optional character prefix for output file names.
symbolColumn	character with column name of Gene Symbols in dds or NULL.
sampleColumn	character with column name of Sample names in dds
groupColumn	character with column name of group names in dds. Group names must match comparisons!
add_anno_columns	character with names of feature annotation columns given in dds, which shall be added to the output tables. Omitted if NULL.
venn_comparisons	character vector or (named) list of character vectors with group comparisons to be included in Venn Diagram (max 5 comparisons per Venn diagramm). Must be subset of comparisons or NULL.
maxHM	(numeric) max number of top diff. regulated elements printed in Heatmap
scale	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none (default). Either "none", "row" or "column".
HMcexRow	labelsize for rownames in Heatmap
HMcexCol	labelsize for colnames in Heatmap
figure.res	numeric resolution for png.
HMincludeRelevantSamplesOnly	(boolean) if TRUE include only Samples in heatmap, which belong to the groups of the respective group comparison. If FALSE, all samples are plotted in the heatmaps. If a custom selection of sample groups is required for the heatmap of each group comparison, HMincludeRelevantSamplesOnly can be a named list of the form list("groupA-groupB" = c("groupA", "groupB", "groupX"))
color.palette	select color palette for heatmaps

Details

Function uses the DESeq2 package for differential expression analysis of an un-normalized, un-transformed DESeqDataSet. Analysis is performed for any number of group comparisons. The group designations in the groupColumn must match the contrasts given in comparisons ("groupA-groupB"). P-value and foldchange thresholds may be applied to filter result data. Volcano plots are generated for each group comparison given in comparisons with highligted significance thresholds. For generation of heatmaps, the count data is log2-transformed. Heatmaps are generated for top differentially expressed genes for each group comparison.

Value

List of elements

• DEgenes list of dataframes with differential expressed genes according to significance thresholds for each comparison (sorted by p-value). List elements are named by the respective group comparison.

• DEgenes.unfilt list of dataframes with unfiltered differential expression data for each comparison (sorted by p-value).

Filtered and unfiltered result tables, heatmaps, MA-plots and volcano plots for each group comparison as well as dispersion plot and Venn diagrams are stored as side-effects in the project folder.

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.