Description Usage Arguments Details Value Author(s)
View source: R/GEX_wrapDESeq2.R
Differential Gene expression analysis for multiple group comparisons incl. output of Venn diagrams, volcano plots and heatmaps.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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"
)
|
dds |
DESeqDataSet |
comparisons |
character vector with group comparisons in format |
min_rowsum |
numeric. Minimum rowsum of countmatrix of |
p_value_threshold |
numeric p-value threshold |
adjust.method |
adjustment method for multiple testing ( |
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 |
sampleColumn |
character with column name of Sample names in |
groupColumn |
character with column name of group names in |
add_anno_columns |
character with names of feature annotation columns given in |
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 |
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 |
HMcexRow |
labelsize for rownames in Heatmap |
HMcexCol |
labelsize for colnames in Heatmap |
figure.res |
numeric resolution for png. |
HMincludeRelevantSamplesOnly |
(boolean) if |
color.palette |
select color palette for heatmaps |
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.
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.
Frank Ruehle
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