.sapiens, names(gxs), "SYMBOL", "ENTREZID") :
> could not find function "mapIds"
>
> Where can I find this function?
>
> > SomeGenes <- gxs[ c("HRAS", "WT1", "IGF2") ]
> Error: object 'gxs' not found
>
&
quot;ENTREZID")
>> Error in mapIds(Homo.sapiens, names(gxs), "SYMBOL", "ENTREZID") :
>> could not find function "mapIds"
>>
>> Where can I find this function?
>>
>> > SomeGenes <- gxs[ c("HRAS", "WT1",
:00:41
Aan: Mulder, R
CC: Tim Triche, Jr.; bioc-devel@r-project.org
Onderwerp: Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS
data in r
This has been a very interesting and illuminating dialogue but it really should
be moved to
support.bioconductor.org<https://eu
ot;mapIds"
>
> Where can I find this function?
>
> > SomeGenes <- gxs[ c("HRAS", "WT1", "IGF2") ]
> Error: object 'gxs' not found
>
> Does this have to do with the fact that IGF2 is not included in my panel?
>
> > sbparam <- S
;IGF2") ]
Error: object 'gxs' not found
Does this have to do with the fact that IGF2 is not included in my panel?
> sbparam <- ScanBamParam(which=SomeGenes)
Error in ScanBamParam(which = SomeGenes) : object 'SomeGenes' not found
As a result of the previous error, right?
Interestingly
Do you perhaps have ideas on how I could do this?
>
> Best,
>
> Rene
>
> --------------
> *Van:* Tim Triche, Jr.
> *Verzonden:* vrijdag 6 maart 2020 13:57:10
> *Aan:* Mulder, R
> *CC:* bioc-devel@r-project.org
> *Onderwerp:* Re: [Bioc-devel] MRD measu
3:57:10
Aan: Mulder, R
CC: bioc-devel@r-project.org
Onderwerp: Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS
data in r
Oh hey, one last thing — if all you want is to get nucleotide counts per region
of interest, just use pileup() in Rsamtools, with bamWhich(GRanges) holding a
GRanges
Oh hey, one last thing — if all you want is to get nucleotide counts per region
of interest, just use pileup() in Rsamtools, with bamWhich(GRanges) holding a
GRanges (Genomic Ranges) of your regions added to scanBamParams for each BAM.
It sounds awkward but in practice it is super fast and will
donderdag 5 maart 2020 22:37
> Aan: Mulder, R
> CC: bioc-devel@r-project.org
> Onderwerp: Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS
> data in r
>
> a few thoughts:
>
> 1) look into Shearwater
> (https://bioconductor.org/packages/release/bioc/htm
a few thoughts:
1) look into Shearwater (
https://bioconductor.org/packages/release/bioc/html/deepSNV.html), then
2) talk to Todd Druley @ WashU, Elli Pappaemanuil @ MSKCC, Ruud & Bob @
Erasmus, the usual suspects
3) plan to validate w/ddPCR (at the absolute very least) and be aware that
most
Hi,
I was wondering if anyone could help me with a script and support for the above
mentioned goal.
For this I have several BAM files for which I want to determine de nucleotide
count per region of interest. The latter could be several hotspot mutation
sites. I would like to get an overall
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