FourCSeq - how to write tables with the results
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@francesclopez-8907
Last seen 5.9 years ago
United States

Hi, 

I went through the whole workflow and I would like to print tables with the data in results and fcf objects. How can I do that?

One table could include sample wise information with zscores, p-values, counts and the other with the differences between conditions. I have 2 reps for each of the 3 conditions. 

Ideally, I would like to see the peaks/interactions with chr and coordinates (chr, start, end).

Is there an easy way to add the closest or overlapped feature in the genome? using TxDb.Hsapiens.UCSC.hg19.knownGene?

As far I understand this method only looks at interactions within the same chromosome (no trans interactions) right?

I am not an expert on R as you noticed.

Thank you very much for your time and help,

Francesc

fourcseq • 942 views
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felix.klein ▴ 150
@felixklein-6900
Last seen 3.1 years ago
Germany

Hello Francesc,

as first step I would recommend to look into the pdf vignette of the package. There are some examples how the data can be extracted.

Here is a short summary of the things I think you are looking for:

You can extract the genomic information about the fragments (GRanges Object) with the following command:

frags <- rowData(fcf)

This contains quite some information from intermediate steps. If you only want the positions use this:

mcols(frags) <- NULL

To extract the zscores (as matrix) from the Object run this command:

zScore <- assay(fcf, "zScore")

And to merge it with the genomic positions it has to be transformed to a DataFrame and then can be attached to mcols of the GRanges object.

mcols(frags) <- cbind(mcols(frags), DataFrame(zScore))

frags

For the other assays you can do this as well. Which assays there are can be checked by this:

names(assays(fcf))

 

For the differential analysis you get the results like this:

results <- getAllResults(fcf)
head(results)[,1:6]

 

I hope this answers your questions. There are some nice tutorials how to work with GRanges and SummarizedExperiments (which is the class on which FourCSeq builds on). Have a look at those as well to get more familiar with them

Best regards,

Felix

 

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Hi Felix,

I was wondering when running results <- getAllResults(fcf) is there an option to also export the genomic location for each test as one of the columns? 

Thanks,

Fides

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Hello Fides, could you please specify what you exactly mean by this? Felix On 06/14/2016 09:01 AM, fidlay [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User fidlay <https: support.bioconductor.org="" u="" 10894=""/> wrote Comment: > FourCSeq - how to write tables with the results > <https: support.bioconductor.org="" p="" 72982="" #83766="">: > > Hi Felix, > > I was wondering when running results <- getAllResults(fcf) is there an > option to also export the genomic location for each test as one of the > columns? > > Thanks, > > Fides > > ------------------------------------------------------------------------ > > Post tags: fourcseq > > You may reply via email or visit > C: FourCSeq - how to write tables with the results >
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Hi Felix, 

Sorry for the delayed reply --

What I meant was that when I used getAllResults, the output I am getting is a data frame or table whose first 6 columns are these: 

head(results[,1:6])

"baseMean"    "log2FoldChange_ctrl_essrb_kd"    "lfcSE_ctrl_essrb_kd"    "stat_ctrl_essrb_kd"    "pvalue_ctrl_essrb_kd"    "padj_ctrl_essrb_kd"

It tells me the log fold change and the statistics, but since there is no genomic location, I don't know which interactions corresponds to where relative to bait. 

Thanks!

Fides

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Hello Fides,

this is straight forward, since results has the same dimensions as the FourCSeq object. So you can get the genomic coordinates with `rowRanges(fcf)` from there and join it to the results.

combinedData <- cbind(as.data.frame(rowRanges(fcf)), results)

Best regards,

Felix

 

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Great - thank you!

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@francesclopez-8907
Last seen 5.9 years ago
United States

Thanks for all your help. 

I used this to annotated with genes that overlapped the coordinates.

Mapping genome regions to gene symbols

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ferbecneu • 0
@ferbecneu-16188
Last seen 10 months ago

Hi Felix I tried doing what you advised with combinedData <- cbind(as.data.frame(rowRanges(fcf)), results) 

and also with mcols(frags) <- cbind(mcols(frags), DataFrame(zScore))  but I get the error:

Error in DataFrame(..., check.names = FALSE) : 
  different row counts implied by arguments

Do you know how can I solve this?

Thanks!

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