User: Fabio Marroni
Fabio Marroni • 2.3k
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Posts by Fabio Marroni
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... I cannot see the figures, is it me or something went wrong? ...
written 1 day ago by
Fabio Marroni • 2.3k
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... 1) Why do you need to use PowerMarker? It is very old and not maintained since several years. There are a lot of tools for performing association analysis.
2) Can you provide a small input example and the error you get? You are more likely to get help after providing this information. ...
written 1 day ago by
Fabio Marroni • 2.3k
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Comment:
C: Bedtools fisher result
... The strange thing is that the counts for "not in -a" (second row of the 2 by 2 contingency table) are zero. I would suggest to check this issue ...
written 2 days ago by
Fabio Marroni • 2.3k
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... Try something like `dataSub <- dataSub[order(dataSub$L2FC),]` (assuming L2FC is the log2fold change column).
As an alternative, you might just let the algorithm cluster them for you by using `pheatmap(dataSub, annotation_col = anno, cluster_rows=TRUE, cluster_cols=FALSE, fontsize=24)`
...
written 24 days ago by
Fabio Marroni • 2.3k
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... If you are missing a lot of hits, but getting some, then is just a sensitivity problem.
Try to understand what parameters are used on the webserver and use exactly those. Otherwise, you can just slightly relax your evalue.
...
written 24 days ago by
Fabio Marroni • 2.3k
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... A test that I usually perform is to run the command with a very small dataset and check if the problem persist. If it persists, then it might be some problem with data format.
...
written 24 days ago by
Fabio Marroni • 2.3k
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... [i.sudbery][1] is `time -v` specific for WSL?
I tried it, because it could be useful for me, but it resulted in printing the time and the error: `bash: -v: command not found`.
What can the problem be?
[1]: https://www.biostars.org/u/16790/ ...
written 24 days ago by
Fabio Marroni • 2.3k
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... Out of curiosity: why do you want to use association instead of linkage or transmission-disequilibrium test?
This said, you might search the literature for "family-based association test", there are several tools around.
I remember using [FBAT][1]
[1]: https://sites.google.com/view/fbat-web-pa ...
written 24 days ago by
Fabio Marroni • 2.3k
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Comment:
C: software to draw the picture
... I don't think so.
Infopath (according to [this][1] tutorial) can do several things, but is not very powerful for even simple graphs. As [ATpoint][2] suggested, you can use Illustrator, Inkscape, PowerPoint or Libreoffice Impress, or Libreoffice Draw. You could also try microsoft paint.
[1]: htt ...
written 25 days ago by
Fabio Marroni • 2.3k
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Answer:
A: Nested data frames in a list
... Try this for creating the list of data.frames.
t=c("B","F","L","I","M","S")
cm.f=list()
for (i in 1:6)
{
a= data.frame("OoenG" = rownames(cm), cm[,grep(t[i], colnames(cm))]);
a$mysum<-apply(a[,2:4],1,sum)
#Remove rows i which the sum is smal ...
written 28 days ago by
Fabio Marroni • 2.3k
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