User: Haiying.Kong

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Haiying.Kong30
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Germany
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Posts by Haiying.Kong

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warnings: closing unused connection
... I am using cn.mops package to identify CNVs. If I run: read.counts = getSegmentReadCountsFromBAM(BAMFiles=bam.files, sampleNames=sam.names, GR=gr, parallel=30) The output looks fine, but I get warnings: There were 30 warnings (use warnings() to see them) > warnings() Warning messages: 1: clos ...
parallel computation written 21 hours ago by Haiying.Kong30 • updated 7 hours ago by Charles Plessy20
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Comment: C: Reading Large File in Trunk
... That looks much better. Thank you so much  :) ...
written 11 days ago by Haiying.Kong30
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Comment: C: Reading Large File in Trunk
... Even if I use readLines, it was not as slow as what I thought. This works fine  :) Thank you very much for your help.   apple = c() fl = file(maf.file, "r") repeat { aster = readLines(fl, trunk.size) if (length(aster) == 0) break idx.del.line = c(grep("^#", aster), grep("Hugo_Symbol", ...
written 11 days ago by Haiying.Kong30 • updated 11 days ago by Martin Morgan ♦♦ 19k
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Comment: C: Reading Large File in Trunk
... if there are no more lines left, I get error message. I could use try(read.table....), but there risk that I would treat errors from file format as error for no more lines left. The file is maf file, so it is not very well structured. ...
written 11 days ago by Haiying.Kong30
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Comment: C: Reading Large File in Trunk
... ********************************************************************************************************************* My mistake. read.table takes care for the problem. nrows: integer: the maximum number of rows to read in. *********************************************** ...
written 11 days ago by Haiying.Kong30
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Comment: C: Reading Large File in Trunk
... Thank you so much for your most prompt help  :) I was about to switch to another work, because I thought it could take at least one day before any one could reply with helpful information. ...
written 12 days ago by Haiying.Kong30
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Reading Large File in Trunk
...   I need to read in a large file which is about 77G in txt format, with about 50M lines.   I can use read.table function, and set parameters skip and nrows to read the file in trunk. But this will repeatedly count lines each time I read in a trunk.   Is there any function that can set something si ...
R written 12 days ago by Haiying.Kong30 • updated 12 days ago by Martin Morgan ♦♦ 19k
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Comment: C: loading vcf with readVcf
... After reading in (ignored the warning for a moment), I filtered with filterVCF, and saved as new vcf. But it has wrong information on the column ID: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  T127554 T136801 T78254  T9      T96096  T99633 7       132011577       7:1320 ...
written 14 days ago by Haiying.Kong30
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loading vcf with readVcf
...   I have a vcf file like: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  T127554 T136801 T78254  T9      T96096  T99633 1       10492   .       C       T       40.17   .       AC=1;AF=0.125;AN=8;BaseQRankSum=-4.310e-01;ClippingRankSum=0.00;DP=10;ExcessHet=3.0103;FS=4.771;ML ...
bioconductor written 14 days ago by Haiying.Kong30 • updated 14 days ago by James W. MacDonald43k
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Operation on GRanges Object
... ******************************************************************************************************************* I figured out, and tried to delete the post, but no option for deleting. The answer is: rowRanges(all)@elementMetadata has all information on the right hand side of bar separation. ...
bioconductor written 17 days ago by Haiying.Kong30 • updated 17 days ago by Martin Morgan ♦♦ 19k

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