aman21392
commented
3 years ago I also run test data but I did not find how I get the differential expression gene list.
library(circMeta) CIRI.files=c( "/Drive1/DBT_data/differentially_expression_DEseq2/circmeta/test_data/cerebellum/CIRI1.circ", "/Drive1/DBT_data/differentially_expression_DEseq2/circmeta/test_data/cerebellum/CIRI2.circ", "/Drive1/DBT_data/differentially_expression_DEseq2/circmeta/test_data/frontcortex/CIRI1.circ", "/Drive1/DBT_data/differentially_expression_DEseq2/circmeta/test_data/frontcortex/CIRI2.circ") designs=c(0,0,1,1) fdr.level=0.05 res1=circJuncDE(CIRI.files[c(1,2,3,4)],designs,circ.method='CIRI',DE.method='pois.ztest') Add closest gene...... Add circRNA class...... Add junction/nonjunction reads...... id1=rownames(res1)[res1$fdr<fdr.level] res2=circJuncDE(CIRI.files[c(1,2,3,4)],designs,circ.method='CIRI',DE.method='edgeR') Add closest gene...... Add circRNA class...... Add junction/nonjunction reads...... id2=rownames(res2)[res2$fdr<fdr.level] res3=circJuncDE(CIRI.files[c(1,2,3,4)],designs,circ.method='CIRI',DE.method='DESeq2') Add closest gene...... Add circRNA class...... Add junction/nonjunction reads...... converting counts to integer mode id3=rownames(res3)[res3$fdr<fdr.level] id1=rownames(res1)[res1$fdr<fdr.level] length(id1) [1] 406 id2=rownames(res2)[res2$fdr<fdr.level] length(id2) [1] 4 id3=rownames(res3)[res3$fdr<fdr.level] length(id3
- ) [1] 4 length(intersect(id1,id3)) [1] 4 length(intersect(id2,id3)) [1] 3 length(intersect(id1,id2)) [1] 4
So please can you tell me how I get the differential expressed gene list in any sample.
This error occur during circJuncDE script use:-
res1=circJuncDE(CIRI.files[c(1,2,3,4)],designs,circ.method='CIRI',DE.method='pois.ztest') Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 5822: at least two out of 'start', 'end', and 'width', must be supplied.