Hi,
I want to use segChrom() method in tilingArray package. For that I need to
create a probeAnno object. I could not find much much info by ?probeAnno. I need
help in creating probeAnno object.
Snap shot of the file(.txt):
chr1 2500014 2500038 + 0.232689943122845
chr1 2500039 2500063 + 2.60502410304227
chr1 2500062 2500086 + 0.0756595313279895
chr1 2500080 2500104 + 0.78574617788405
chr1 2500122 2500146 + 0.57901385309105
chr1 2500143 2500167 + 0.443992729102625
chr1 2500163 2500187 + 0.538200424867007
chr1 2500183 2500207 + 1.50024545788701
chr1 2500205 2500229 + 0.152549915278444
Thanks in advance.
Regards,
Ambuj A Thacker
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Hello Ambuj,
I found some information about probeAnno in the packages ccTutorial,
davidTilling and Ringo.
Objects can be created by calls of the form new("probeAnno", map,
arrayName, genome).
map:
Object of class "environment" This map consists of four vectors
for
each chromosome/strand, namely, say for chromosome 1:
1.start
genomic start coordinates of probe matches on chromosome 1
1.end
genomic start coordinates of probe matches on chromosome 1
1.index
identifier of probes matching at these coordinates
1.unique
vector of the same length as the three before; encoding how
many matches the corresponding probe has in the given file or
data.frame. An entry of '0' indicates that the probe matching at this
position has only this one match.
arrayName:
Object of class "character", the name or identifier of the
microarray design, e.g. 2005-06-17\_Ren\_MM5Tiling\_Set1
genome:
Object of class "character", which genome the reporters have been
mapped to
pa <- new("probeAnno")
pa["X.start"] <- seq(5000,10000,by=1000)
if (interactive()) show(pa)
I hope this help.
Regards,
Viviana
Hi,
??????????? Thank you Viviana for the description to create probeAnno object.
The below link was very helpful:
http://svitsrv25.epfl.ch/R-doc/library/Ringo/html/probeAnnoClass.html
I tried creating the object in the following ways where: startProbe &
endProbe are the vectors which has the genomic start co-ordinates and end
co-ordinates and index is a vector to store identifier of the probes.
intensityData is the vector that stores data to be segmented
Method 1.>map<-new("environment",startProbe,endProbe,index)
>arrayName<-"2009_01_18_veg1028_w"
>genome<-"genome"
>probeAnnotation<-new("probeAnno",map,arrayName,genome)
>segEnv<-segChrom(intensityData,probeAnno=probeAnnotation,chr="1",strands="+",nrBasesPerSegment=750)
Running 'segment' on chromosome 1.+Error in mget(paste(chrstrd[j], what,
sep = "."), probeAnno) : ? second argument must be an environment
Method 2.> pa3<-posToProbeAnno("~/523/POSFormat_tab.csv");Creating
probeAnno mapping for chromosome 1 Done.
> arrayName(pa3)<-"S.Pombe"
> genome(pa3)<-"genome"
> show(pa3)
A 'probeAnno' object holding the mapping between reporters and genomic
positions.
Chromosomes: 1
Microarray platform: S.Pombe
Genome: genome>segEnv<-segChrom(intensityData,probeAnno=pa3,chr="1",strands="+",nrBasesPerSegment=750)
Running 'segment' on chromosome 1.+Error in mget(paste(chrstrd[j], what,
sep = "."), probeAnno) : second argument must be an environment
Both the methods gave the same error "second argument must be an
environment". I am unable to execute segChrom() of tilingArray package. Any
sugetions would be helpful. Thanks in advance.
Regards,
Ambuj A Thacker
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