User: li lilingdu

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li lilingdu450
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Posts by li lilingdu

<prev • 48 results • page 1 of 5 • next >
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Question about parallel manipulation on CharacterList objects
... Hi, I want to know how to parallelly manipulate CharacterList objects in IRanges package. For example, for very large list of letters: ir = successiveIRanges(width=sample(1:26,1000000,replace=T)) dat = relist(sample(letters,sum(width(ir)),replace=T),ir) For each element of the length-1000000-Ch ...
iranges s4vectors written 14 months ago by li lilingdu450 • updated 14 months ago by Martin Morgan ♦♦ 20k
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Answer: A: unused argument (organism="human")
... Your document might be obsolete. you can install the latest clusterProfiler package, and look at the help info for function groupGO where the 2nd parameter should be  OrgDb (the meta package name) groupGO(gene, OrgDb, keytype = "ENTREZID", ont = "CC", level = 2, readable = FALSE) ...
written 14 months ago by li lilingdu450
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Comment: C: Gviz: How to control `grid` parameter and how to add horizontal lines with diffe
... But it will be greater to list/get the viewports and even the correspondence of grobs and viewports in the plot, so more detailed and flexible control of the plot can be achieved.  For task such as http://stackoverflow.com/questions/25494125/plotting-arbitrary-lines-at-gviz-plottracks would be poss ...
written 14 months ago by li lilingdu450
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Comment: C: Gviz: How to control `grid` parameter and how to add horizontal lines with diffe
... Just for add of horizon lines: plotTracks(dTrack,baseline=c(-5,0,5),col.baseline=c('red','green','blue')) ...
written 14 months ago by li lilingdu450
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Answer: A: Gviz: How to control `grid` parameter and how to add horizontal lines with diffe
... Solution I considered is to add grid grills firstly and then modify their positions , following is the code, but another problem occur: library(Gviz) ########using the example data contained in Gviz data(twoGroups) dat<-resize(twoGroups,width=1) dat<-dat[,'control'] dTrack <- DataTrack ...
written 14 months ago by li lilingdu450
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Answer: A: Howto: View Pileup or Base level stats in R using Rsamtools or rbamtools
... Hi, Some functions in Rsamtools and GenomicAlignments package can fullfil this task. Following were from the help document of GenomicAlignments package 1 stackStringsFromBam function for stacking the read sequences (or their quality strings) stored in a BAM file on a region of interest. 2 pileLe ...
written 14 months ago by li lilingdu450
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Answer: A: Gviz Color Filling
... load and use the geneModels data included in the package as examples, we only focus on two transcripts: library(Gviz) data(geneModels) geneModels[geneModels$transcript %in% c('ENST00000487720','ENST00000481204'),]->dat And set the filled color as the default #FFD58A for all exons except of fo ...
written 14 months ago by li lilingdu450
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After mapping one Sanger sequence read (about 900bp) to hg19 using blastn, How can I get variants presented as reference-based position and base change with the blastn output file?
... Hi, After mapping one Sanger sequence read (about 900bp) to hg19 using blastn of NCBI, How can I get  variants presented as reference-based position and base change with the blastn output file such as XML output or asn1 output? For example, Query 7 GAAAG--AACAGGCT-ACAATTTTGGACTCTGGTCTCT ...
variantannotation biostrings blast written 15 months ago by li lilingdu450
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Comment: A: Genes found on particular chromosome using two methods in TxDb.Hsapiens.UCSC.hg
... And further problems might be occur: we want to find some overlaps with particular genomic fragement load the library library(TxDb.Hsapiens.UCSC.hg19.knownGene) TxDb.Hsapiens.UCSC.hg19.knownGene->txdb the fragment GRanges('chr6',IRanges(29624758,33160245),strand="+")->ir genome(ir)< ...
written 15 months ago by li lilingdu450 • updated 15 months ago by Martin Morgan ♦♦ 20k
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Comment: A: Genes found on particular chromosome using two methods in TxDb.Hsapiens.UCSC.hg
... And indeed I found the 1000 gene found by both methods were located at chromosome 6 while the 207 genes missed by the 2nd methods were located at  chr6_apd_hap1  ,chr6_cox_hap2  ,chr6_dbb_hap3 , chr6_mann_hap4  ,chr6_mcf_hap5  ,chr6_qbl_hap6 ,chr6_ssto_hap7  besides chr6 (all 207 genes on chrorm ...
written 15 months ago by li lilingdu450

Latest awards to li lilingdu

Scholar 6.7 years ago, created an answer that has been accepted. For A: GRanges get hits from (only) antisense strand with findOverlaps().
Scholar 6.7 years ago, created an answer that has been accepted. For A: Gviz: How to control `grid` parameter and how to add horizontal lines with diffe

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