User: salamandra

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salamandra0
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Posts by salamandra

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draw.pairwise.venn: Misplaced line connecting external area label
... Hi, in venn diagram here the line connecting external intersection area label to its anchor point is misplaced, does anyone know what parameter of the function draw.pairwise.venn corrects for this? png(paste0(dir,condition[j],'.Human.MEF',timecorr[i], '_vennNumber.png'), res = 300, height = 20*30 ...
venndiagram written 4 weeks ago by salamandra0
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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 17 months ago by salamandra0
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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 17 months ago by salamandra0
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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 20 months ago by salamandra0

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