User: Papyrus
Papyrus • 680
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Posts by Papyrus
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... I'd say the way to handle it depends on the biological question at hand. Indeed, merging strands focuses on the CpG sites and ignores hemimethylation. On the other hand, the great majority of studies on DNA methylation focus on CpG sites and do not study hemimethylation.
Is the study of hemimethyla ...
written 14 days ago by
Papyrus • 680
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... Glad to know it worked out in the end!
Indeed, the names of the elements of the list (element `my_colour$condition` in this example) must match the columns of your annotation `df` (column `df$condition`). And the names of the vector of colors within each element in the list ( `CD4T_KO_NS` `CD4T_KO ...
written 16 days ago by
Papyrus • 680
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... In that example it reads `conditions`, but it should be `condition`. Did you check that?
This example works for me:
counts <- matrix(1:8,4,2)
colnames(counts) <- c("l1","l2")
rownames(counts) <- c("a","b","c","d")
my_colour <- list(condition = c(l1 = "orange", l2 = "sky ...
written 17 days ago by
Papyrus • 680
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... It's a bit hard to see within the loop structure, and without showing your error message, but I believe your problem may be that when you create the list to define your colors:
my_colour = list(df=c(l1="orange", l2="skyblue"))
The internal variable should be named like the column of the annota ...
written 20 days ago by
Papyrus • 680
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... I believe this refers to merging the counts of the cytosines for that CpG site. Both the C at the + strand, and the other C at the - strand (minus 1 position) belong to the same CpG site. They are not 2 different CpG sites (you could look at the site from the perspective of the "+" strand or of the ...
written 21 days ago by
Papyrus • 680
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... Also, if you are specifically interested in GO terms and have too many, there are some tools which will reduce and summarize redundant lists of the terms, such as REViGO. ...
written 22 days ago by
Papyrus • 680
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... intersect(dataframe1$gene_column, dataframe2$gene_column)
(but not actually a bioinfo question) ...
written 23 days ago by
Papyrus • 680
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... Sorry, I just mentioned that for the sake of explaining why "information" about covariates such as batches may be in genes which are not the subset of genes of interest (for example see the [RUVSeq][1] package). But this is not directly related to your question, I did not mean to be confusing. These ...
written 25 days ago by
Papyrus • 680
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... If you want to know about batch effects, which are often methodological, or in general any covariate, I think you should investigate on all of the genes because those type of biases will be present in all of your genes (i.e. your genes of interest a priori should not be biased towards being more or ...
written 26 days ago by
Papyrus • 680
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... No, I meant to say the same thing that Kevin (much more clearly) stated: that you should set the same p-value, q-value thresholds (to 1, to capture all the results), to really compare, because the functions may be filtering the results differently.
If, after checking that the functions are being us ...
written 29 days ago by
Papyrus • 680
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For A: What to choose as background genes in GO enrichment analysis
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For A: What to choose as background genes in GO enrichment analysis
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For A: Unable to perform for loop over list of GRanges
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For A: Unable to perform for loop over list of GRanges
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For A: Unable to perform for loop over list of GRanges
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For A: What to choose as background genes in GO enrichment analysis
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For A: Unable to perform for loop over list of GRanges
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For A: What to choose as background genes in GO enrichment analysis
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For A: Unable to perform for loop over list of GRanges
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