[BioC] questions on cghMCR package

Fri Jan 13 17:51:24 CET 2012

Hi Nathalie -- it often helps to include the package maintainer in email 
(I added the maintainer to this email), to draw their attention to the 
issue.

packageDescription("cghMCR")$Maintainer

Martin

On 01/13/2012 07:13 AM, nathalie wrote:
> HI , could I get your views on this please, is this package still used?
> thanks a lot
> Nat
>
> -------- Original Message --------
> Subject: seeking help on cghMCR pleeeease
> Date: Mon, 12 Dec 2011 14:17:58 +0000
> From: Nathalie Conte<nac at hinxton.sanger.ac.uk>
> To: bioconductor at r-project.org
>
> HI,
> I am using cghMCR and I would need some advice on the software
> behaviour. I don't seem to get any different results when I change the
> gapAllowed parameter.
> I have used DNAcopy to create a segmented data for all my samples. Then
> I choose to use cghMCR to get common alterations between my samples.
> These are all arguments from the package doc(latest version):
>
> segments is a data frame extracted from the "output" element
> of the object
> returned by segment of the package DNAcopy or getSegments
>
> gapAllowed is an integer specifying low threshold of base
> pair number to
> separate two adjacent segments, belower which the two
> segments will be joined
> as an altered span
>
> alteredLow is a positive number between 0 and 1 specifying
> the lower resh-
> old percential value. Only segments with values falling
> below this threshold are
> considered as altered span
>
> alteredHigh is a positive number between 0 and 1 specifying
> the upper resh-
> old percential value. Only segments with values falling over
> this threshold are
> considered as altered span
>
>
> recurrence is an integer between 1 and 100 that specifies
> the rate of occur-
> rence for a gain or loss that are observed across sample.
> Only gains/losses with
> ocurrence rate grater than the threshold values are
> declared as MCRs
>
> spanLimit is an integer that defines the leangh of altered
> spans that can be
> considered as locus. It is not of any use at this time
>
> thresholdType is a character string that can be either
> "quantile" or "value"
> indicating wether alteredLow or alteredHigh is quantial or
> actual value
>
>
>
> In my analysis, I have used cghMCR with threshold value log2R of low
> -0.25 and high =0.25 , a spanLimit of 2.10^7 and I have tried several
> gapAllowed values, 5, 500 , 5000 and 50000 .Each time I used the MCR
> function to identify the minimum regions. I have put an example of each
> results only on 25 lines of chromosome 4 to avoid massive sized files
> (see attached) , but basically whatever the gapAllowed size i get the
> same MCRs at the end for all postitions. I would expect this to vary as
> segments should be fused together differently given this parameter..
> Could you please help with this and advise on what I might be doing wrong?
> Is spanLimit any use? in the doc, It is written "It is not of any use
> at this time"??
> Another point, the gapAllowed is specified " is an integer specifying
> low threshold of base pair number " is the unit in base pair number, in
> several examples it seems that the units are in kb???
>
>
> thanks a lot ,
>
> code for gapAllowed=5
> ##get the cghMCR function with these parameters
> cghmcr0.25T_5k_2_20M_sdundo1.5<- cghMCR(sdundo.segData_order1.5,
> gapAllowed = 5, alteredLow = -0.25,alteredHigh = 0.25,
> spanLimit=20000000,recurrence=2,thresholdType=c("value"))
> ##identify the MCRs
> mcrs0.25T_5k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5k_2_20M_sdundo1.5)
> mcrs0.25T_5k_2_20M_sdundo.bind1.5<-cbind (
> mcrs0.25T_5k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start",
> "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] )
> write.table(mcrs0.25T_5k_2_20M_sdundo.bind1.5,
> file="PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F)
> PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5.txt",
>
>
> sep="\t", header=T)
> ##only 25 lines of chromsome 4
> test.5k=head(PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5==4,],25)
>
> ##attached data
> write.table(test.5k, file="test.5k.txt", sep="\t")
>
> code for gapAllowed=500
> cghmcr0.25T_500k_2_20M_sdundo1.5<- cghMCR(sdundo.segData_order1.5,
> gapAllowed = 500, alteredLow = -0.25,alteredHigh = 0.25,
> spanLimit=20000000,recurrence=2,thresholdType=c("value"))
> mcrs0.25T_500k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500k_2_20M_sdundo1.5)
> mcrs0.25T_500k_2_20M_sdundo.bind1.5<-cbind (
> mcrs0.25T_500k_2_20M_sdundo1.5[, c ( "chromosome", "status",
> "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] )
> write.table(mcrs0.25T_500k_2_20M_sdundo.bind1.5,
> file="PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F)
> PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5.txt",
>
>
> sep="\t", header=T)
> test.500k=head(PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5==4,],25)
>
> write.table(test.500k, file="test.500k.txt", sep="\t")
>
> code for gapAllowed=5000
> cghmcr0.25T_5000k_2_20M_sdundo1.5<- cghMCR(sdundo.segData_order1.5,
> gapAllowed = 5000, alteredLow = -0.25,alteredHigh = 0.25,
> spanLimit=20000000,recurrence=2,thresholdType=c("value"))
> mcrs0.25T_5000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5000k_2_20M_sdundo1.5)
> mcrs0.25T_5000k_2_20M_sdundo.bind1.5<-cbind (
> mcrs0.25T_5000k_2_20M_sdundo1.5[, c ( "chromosome", "status",
> "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] )
> write.table(mcrs0.25T_5000k_2_20M_sdundo.bind1.5,
> file="PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F)
> PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5.txt",
>
>
> sep="\t", header=T)
> test.5000k=head(PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5==4,],25)
>
> write.table(test.5000k, file="test.5000k.txt", sep="\t")
>
> code for gapAllowed=500000
> cghmcr0.25T_500000k_2_20M_sdundo1.5<- cghMCR(sdundo.segData_order1.5,
> gapAllowed = 500000, alteredLow = -0.25,alteredHigh = 0.25,
> spanLimit=20000000,recurrence=2,thresholdType=c("value"))
> mcrs0.25T_500000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500000k_2_20M_sdundo1.5)
> mcrs0.25T_500000k_2_20M_sdundo.bind1.5<-cbind (
> mcrs0.25T_500000k_2_20M_sdundo1.5[, c ( "chromosome", "status",
> "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] )
> write.table(mcrs0.25T_500000k_2_20M_sdundo.bind1.5,
> file="PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5.txt", sep="\t",
> row.names=F)
> PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5.txt",
>
>
> sep="\t", header=T)
> test.500000k=head(PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5==4,],25)
>
> write.table(test.500000k, file="test.500000k.txt", sep="\t")
>
> sessioninfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=C
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] cghMCR_1.10.0 limma_3.4.5 CNTools_1.6.0
> genefilter_1.30.0
> [5] DNAcopy_1.22.1
>
> loaded via a namespace (and not attached):
> [1] annotate_1.26.1 AnnotationDbi_1.10.1 Biobase_2.8.0
> [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.13.0
> [7] survival_2.35-8 xtable_1.6-0
>
>
>
>
>
>
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