NetBID
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jyyulab
Data-driven Network-based Bayesian Inference of Drivers
I checked my data and there is no na/nan. However, it still report the error in `draw.emb.kmeans `,as following: Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, : missing values...
Thank you for making such a great tool! When I run the NetBID tutorial, I don't get error when I use the function getDE.BID.2G, but I get a lot of...
In the rare cases when there is a driver which we have DA values for, but whose corresponding gene was not in the expression matrix (resulting in NA values in...
Hi Sherry, We need to update the get_IDtransfer() function to include an argument useCache = F within getBM() function from biomart. I have attached a working version of the modified...
The DA/DE P values show on the plot are different from the ones in the master table. There is a bug when converting Z-score to P value in the plot...
Quitting from lines 75-91 (afterQC_filt0.5_PDX80QC.Rmd) Error in apply(s1, 1, min) : dim(X) must have a positive length In addition: Warning message: In dir.create(outdir, recursive = TRUE) : Error in apply(s1,...
draw.bubblePlot(driver_list= driver_list,show_label=ms_tab[driver_list,'gene_label'], Z_val=ms_tab[driver_list,sprintf('Z.%s_DA',comp_name)], driver_type=ms_tab[driver_list,'gene_biotype'], target_list=analysis.par$merge.network$target_list,transfer2symbol2type=transfer_tab, bg_list=ms_tab[,'geneSymbol'],min_gs_size=5,max_gs_size=500,use_gs="all", top_geneset_number=15,top_driver_number=20, pdf_file = sprintf('%s/bubblePlot2.pdf',analysis.par$out.dir.PLOT), main='Bubbleplot for top driver targets') “Error in xy.coords(x, y) : 'x' and 'y' lengths differ” when I set up draw.bubblePlot>15,...
fix pvWidth=0 problem in draw.funcEnrich.cluster when there are too many genes to plot When geneWidth1 is very large, mr
