gsea_data: Retrieve Gene Set Enrichment Analysis (GSEA) results

In CEMiTool: Co-expression Modules identification Tool

Description

Retrieve Gene Set Enrichment Analysis (GSEA) results

Usage

gsea_data(cem)

## S4 method for signature 'CEMiTool'
gsea_data(cem)

Arguments

cem	Object of class CEMiTool

Value

Object of class list with GSEA data

Examples

# Get example CEMiTool object
data(cem)
# Look at example annotation file
sample_annotation(cem)
# Run GSEA on network modules
cem <- mod_gsea(cem)
# Check results
gsea_data(cem)

Example output

Warning message:
replacing previous import ‘ggplot2::annotate’ by ‘ggpmisc::annotate’ when loading ‘CEMiTool’ 
   SampleName Class
1    X1913_d0    g0
2    X1911_d0    g0
3    X1908_d0    g0
4    X1909_d0    g0
5    X1910_d0    g0
6    X1912_d0    g0
7    X1901_d0    g0
8    X1902_d0    g0
9    X1903_d0    g0
10   X1904_d0    g0
11   X1906_d0    g0
12   X1907_d0    g0
13   X1914_d0    g0
14   X1915_d0    g0
15   X1916_d0    g0
16   X1913_d3    g3
17   X1911_d3    g3
18   X1908_d3    g3
19   X1909_d3    g3
20   X1910_d3    g3
21   X1912_d3    g3
22   X1901_d3    g3
23   X1902_d3    g3
24   X1903_d3    g3
25   X1904_d3    g3
26   X1906_d3    g3
27   X1907_d3    g3
28   X1914_d3    g3
29   X1915_d3    g3
30   X1916_d3    g3
31   X1913_d7    g7
32   X1911_d7    g7
33   X1908_d7    g7
34   X1909_d7    g7
35   X1910_d7    g7
36   X1912_d7    g7
37   X1901_d7    g7
38   X1902_d7    g7
39   X1903_d7    g7
40   X1904_d7    g7
41   X1906_d7    g7
42   X1907_d7    g7
43   X1914_d7    g7
44   X1915_d7    g7
45   X1916_d7    g7
sh: 1: wc: Permission denied
Warning messages:
1: In fgseaMultilevel(...) :
  There were 1 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 10000)
2: In fgseaMultilevel(...) :
  There were 2 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 10000)
$es
         pathway         g0         g3         g7
1             M1 -0.8067205  0.4489329  0.6440414
2             M2  0.7064298 -0.6413889 -0.2499186
3             M3 -0.3591983 -0.7043020  0.5700389
4             M4 -0.4546571  0.8614309 -0.4535420
5 Not.Correlated  0.3443543  0.3876027 -0.3762078

$nes
         pathway        g0        g3        g7
1             M1 -2.541192  2.210005  1.792075
2             M2        NA -2.663619        NA
3             M3 -1.059979 -2.676538  1.511419
4             M4 -1.251358  3.148568 -2.196467
5 Not.Correlated  1.712560  1.531650        NA

$padj
         pathway           g0           g3           g7
1             M1 2.426050e-23 7.302549e-07 5.802028e-08
2             M2           NA 1.014710e-09           NA
3             M3 3.967611e-01 1.015091e-09 2.987307e-03
4             M4 2.154600e-01 1.263564e-12 4.188949e-04
5 Not.Correlated 6.445821e-03 3.874867e-02           NA

CEMiTool documentation built on March 13, 2021, 2 a.m.