Comments (1)
Here is my query data
Browse[1]> v
An object of class "EList"
$genes
ENTREZID SYMBOL length
1 653635 WASH7P 1769
3 645520 FAM138A 1130
5 729737 LOC729737 3402
7 100132287 LOC100132287 4370
13 100133331 LOC100133331 4273
18804 more rows ...
$targets
group lib.size norm.factors
alignment_hg19.10922PP.Aligned.out.sam 0 55574256 1.014363
alignment_hg19.10935PP.Aligned.out.sam 0 51958569 1.025027
alignment_hg19.10973PP.Aligned.out.sam 0 52816361 0.893730
alignment_hg19.10976PP.Aligned.out.sam 0 59232135 1.075921
alignment_hg19.10985PP.Aligned.out.sam 0 58639448 1.075331
16 more rows ...
$E
10922PP 10935PP 10973PP 10976PP 10985PP 11026PP 11045PP 11082PP 11086PP 11103PP 11104PP 11126PP
653635 5.604081 5.039951 5.584493 4.890869 5.011973 5.010928 5.117168 4.799015 4.797974 5.050032 4.945128 4.829888
645520 -4.211382 -4.198488 -3.697884 -3.696114 -4.528971 -3.397952 -3.705004 -6.925601 -3.960871 -4.930459 -4.716059 -5.092687
729737 3.824993 4.609482 3.465280 4.259380 4.203964 4.313154 4.567350 6.089856 3.833042 5.503673 5.119955 5.297468
100132287 4.548351 5.029626 4.109502 4.412113 4.275909 4.654243 4.267375 5.075666 3.979327 4.621285 4.725020 4.915434
100133331 4.975838 5.506088 4.510359 4.908113 4.725369 5.005160 4.690004 5.545907 4.543993 5.173705 5.358027 5.275150
11132PP 11147PP 11160PP 11164PP 11165PP 11182PP 11184PP 11204PP 11218PP
653635 5.039247 4.844473 4.755644 5.588582 5.120050 4.905859 4.843288 4.928274 4.949579
645520 -4.644474 -4.395389 -4.113634 -4.043132 -2.753740 -4.921397 -4.688232 -4.325610 -6.532291
729737 4.773614 4.379706 4.460666 6.712473 4.466282 4.207648 6.322472 3.998379 4.176103
100132287 4.644773 4.208029 4.400928 5.938243 4.711997 4.029551 5.341357 3.689751 4.669379
100133331 5.139895 4.664548 4.926419 6.186561 4.909360 4.738785 5.559488 4.325637 5.058539
18804 more rows ...
$weights
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 21.2429199 20.9413056 21.2037933 21.394000 21.4156158 21.5281834 21.325997 21.1120350 21.1827658 20.9007900 20.9647229
[2,] 0.5964591 0.5779403 0.6111605 0.603389 0.6122545 0.6070699 0.601531 0.5020441 0.5243727 0.4967035 0.5045715
[3,] 17.5303286 17.0085108 12.1745389 19.669321 17.8613489 21.3841895 18.405990 21.9550455 18.5751998 21.4896710 20.6941503
[4,] 18.5823782 18.0794009 15.6762277 19.836502 18.9379667 20.9334772 19.112087 21.0734817 18.3766811 20.1605086 19.5222645
[5,] 20.5738587 20.1943243 18.6399366 21.272716 20.7955789 21.7787045 20.872070 21.8859496 20.7145407 21.5333704 21.2654398
[,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 20.7337806 21.089438 21.2500715 21.7570302 21.3857468 20.1645606 20.7628281 19.3392450 20.600847 20.0333440
[2,] 0.5535584 0.586521 0.5935915 0.5595733 0.5167748 0.4788058 0.5068143 0.4177498 0.491397 0.4742921
[3,] 20.1917869 17.410882 18.5830424 21.8887852 21.8404216 16.6642665 16.1872050 20.4650266 18.684049 16.3105150
[4,] 19.6582995 18.400080 19.1214933 21.2068422 21.5432738 16.5803805 16.7483484 21.7934442 17.979862 16.2933146
[5,] 21.0696960 20.427425 20.8602313 21.9425776 21.9555523 19.4046912 19.6475793 21.9604710 20.370399 19.1927803
18804 more rows ...
$design
high neoadjuvant W
1 1 0 -0.1290363
2 1 0 -0.1270002
3 1 0 -0.4260002
4 1 0 -0.0167777
5 1 0 -0.1356399
16 more rows ...
Browse[1]> contrasts
Contrasts
Levels MUvsWT
high -1
neoadjuvant 1
W 0
Browse[1]> v %$%
+ genes %>%
+ dplyr::select(1:2) %>%
+ setNames(c("FeatureID", "Symbols")) %>% head()
FeatureID Symbols
1 653635 WASH7P
3 645520 FAM138A
5 729737 LOC729737
7 100132287 LOC100132287
13 100133331 LOC100133331
14 100288069 LOC100288069
Cheers
from egsea.
Related Issues (17)
- egsea.ora fails when 'title' has spaces
- Error in Show Pathway
- Error when sort.by not pvals
- Dealing with 'NA' or absent entrezids for rownames in voom object
- Integrating EGSEA plotSummary in Rmarkdown
- Error in initialize(value, ...): l'argomento "go_id" non รจ specificato e non ha un valore predefinito HOT 1
- Typo in man page for showSetByName
- EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed" HOT 1
- Rename entrezIDs into geneIDs in egsea.ora
- Is it possible to use pre-ranked gene lists in EGSEA? HOT 1
- Implement additional visualizations using joyplots
- defensive programming for buildIdx to avoid bad gene sets
- Conversion between the different ID annotations
- Feature Request: More flexible data input
- Feature Request: Improvements to graphic handling
- Feature Request: topSets enhancements
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from egsea.