User: clementpch

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clementpch0
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Posts by clementpch

<prev • 11 results • page 1 of 2 • next >
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Comment: A: Custom matrix building using R from a datafram
... Hi bruce.moran, Thanks a lot for your help, finally you last suggestion work well. I will take in count your advice, thanks. ...
written 25 days ago by clementpch0
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Comment: C: Custom matrix building using R from a datafram
... Sorry but I cannot give you the package because it's a custom packages in devlopment in my lab and the files format of the non-customed package are not the same, so I it will be not usefull for you. I think I didn't be suffisently clear to understand exactly what I want to produce, I mean I want to ...
written 5 weeks ago by clementpch0
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Comment: C: Custom matrix building using R from a datafram
... Hi, Because I have to produce a matrix to have the occurency of each TF type per gene as a gene expression matrix for exemple. Yes I have to produce the two necessary matrix for a package. The issue with this command is that I have not in rowNames the geneID (with no redondancy) and in colnames m ...
written 5 weeks ago by clementpch0
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Comment: C: Custom matrix building using R from a datafram
... Hi, thanks a lot to respond to me. I have do the update on the command that you send me. I have an issue when I launch the command, I think because of the fact that for one gene I have different motifs related to. Here you can see the following terminal error message: > head(geneTF.df) ...
written 6 weeks ago by clementpch0
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Comment: C: Custom matrix building using R from a datafram
... Hi bruce.moran, thanks for your response. I cannot instal the tibble package because I've some issue with the dependency of readr and dplyr already install. so I've used the column_to_rownames() function from the package textshape (v1.7.1). I've launch your code but I have an issues, see bellow th ...
written 6 weeks ago by clementpch0
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Custom matrix building using R from a datafram
... Hi Everyone, I want to produce a matrix which it have in row.names the "gene ID" and in column "Transcription Factor ID" with in value the occurrency of the TF binding related to the nearest gene. So I have produce a data frame with the wanted three information following these commands : ...
R written 6 weeks ago by clementpch0
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Comment: C: Computing gene frequency of specific regions of interest using R
... Thanks a lot for your help Igor. I have convert my gene.bed annotation file into bedgraph (see below an exemple ) : ``` chr1 19056 19132 1 chr1 23012 23989 1 chr1 23990 25394 1 chr1 39764 40757 1 chr1 45872 46172 1 chr1 58908 59872 1 chr1 59875 61036 1 chr1 61803 61875 1 chr1 76843 77041 1 chr1 8 ...
written 8 weeks ago by clementpch0
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Comment: C: Computing gene frequency of specific regions of interest using R
... Ok thanks, I understand I will use awk command to do this. To be sure, I set the data value at 1 for each gene ? I mean the data value correspond to the bed score column ? ...
written 8 weeks ago by clementpch0
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Comment: C: Computing gene frequency of specific regions of interest using R
... Which tool do you used to convert bed to bedgraph please ? I think I will try this options ...
written 8 weeks ago by clementpch0
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Comment: C: Computing gene frequency of specific regions of interest using R
... Hi Igor, I've already try deepTools, the problem with this method is that to plot the density with deeptools you must have a bigWig related to the features in that you want to compute the density for region of interest. But in my case I don't have bigWig of my genes, I just have a bed/gff3/gtf fil ...
written 8 weeks ago by clementpch0

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