Admin: shepherl

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shepherl ♦♦ 130
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Posts by shepherl

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Comment: C: Data analysis in R
... Please load cummeRbund after you installed it:    source("http://bioconductor.org/biocLite.R") biocLite("cummeRbund") library(cummeRbund) cuff_data<-readCufflinks('D:\\AAA-PengZhou\\R-3.0.1\\library\\AAAAAA')   If you are still having trouble, Please also include your sessionInfo()  ...
written 21 days ago by shepherl ♦♦ 130
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Answer: A: problem with makeGRangesListFromFeatureFragments
... You should be able to use unlist and split to get the results you want. If you unlist the grl2 made from myFile2.txt the names on the GRangesList should become the rownames; then split on rowname if you want a GRangesList split by motif name.   ...
written 23 days ago by shepherl ♦♦ 130
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Comment: C: This is post is for testing purposes only.
... Test email  ...
written 6 weeks ago by shepherl ♦♦ 130
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Comment: C: This is post is for testing purposes only.
... Test Number 2 ...
written 6 weeks ago by shepherl ♦♦ 130
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Comment: C: This is post is for testing purposes only.
... This is a test comment  ...
written 6 weeks ago by shepherl ♦♦ 130
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Comment: C: ROPLS error message
... Please try updating to the latest version of R as well as the latest version of the package.  I currently can't reproduce your error when I try using the latest release and latest development versions. If you are still having trouble please provide more detail on how you are loading the package and ...
written 8 weeks ago by shepherl ♦♦ 130
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Comment: C: UTRs position of genomic loci
... I'm having trouble trying to reproduce the code you provided.  #1.UTRs size,   tx_lens$cds_len would be NULL,  unless in the previous call  tx_lens <- transcriptLengths(txdb, with.utr5_len = F, with.utr3_len = T, with.cds_len=F) the argument with.cds_len would have to be changed to TRUE. #G ...
written 10 weeks ago by shepherl ♦♦ 130
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Comment: C: info(header(vcf)) remembers fields not imported: bugfix?
... Thank you for noting this discrepancy. The current implementation of displaying the original header information rather than the subset is deliberate in design.  We felt that knowing all the possible information available from the object could be beneficial. Also some fields are closely related and i ...
written 5 months ago by shepherl ♦♦ 130
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Comment: C: Best way to import from multiple VCF files?
... Please see if some of the errors are corrected when using the devel version.  I just made a few changes so the most current version of the package is GenomicFiles_1.9.12 ...
written 5 months ago by shepherl ♦♦ 130
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Comment: C: Best way to import from multiple VCF files?
... Thank you for the comments.  Are you sure you are using the devel version of Bioconductor: see here Also I am having trouble reproducing some of your errors. Could you share how you created your GRObject    ...
written 5 months ago by shepherl ♦♦ 130

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