User: tania.l.barata

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Posts by tania.l.barata

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Question: Enrichment heatmap - GOstats package of R
... I wanted to build a heatmap with different sets of genes as columns and GO BP terms as rows. The intensity of the colour of each cell in the heatmap would represent the p-value. I started by using hyperGTest of package GOstats to calculate p-value for different GO terms. I selected p-value cutoff a ...
gostats p-value written 4 months ago by tania.l.barata0
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Comment: C: Visualizing GOstats HyperGTest results
... When I did what you suggest it didn't return all GO terms, as the number of GO terms is varying with the gene set. Here is an example: A <- c("86", "51412", "192669", "8289", "57492", "83858", "10533", "10538", "54880", "1230", "947", "79577", "55038", "64866", "1017", "1026", "1063", "1105", ...
written 4 months ago by tania.l.barata0
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What are out-of-bound ranges? Is it necessary to get rid of them?
... With the function: overlaps.anno <- annotatePeakInBatch(overlaps, AnnotationData=annoData, output="nearestBiDirectionalPromoters",bindingRegion=c(-2000, 500)) got this warning message: Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. Warning messages: 1: In v ...
chippeakanno R written 7 months ago by tania.l.barata0

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