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Old 03-31-2015, 06:01 AM   #1
Laquais
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Default RAPIDR package for the NIPT

Hello,

I am a young student. I would like to know where we can integrate the RAPIDR package in a workflow for the NIPT.
Does someone use this package ?

This package uses the human genome reference hg19. Can we use RAPIDR with an other ?

What can be a substitute to RAPIDR in the workflow for NIPT ?

Thanking you in advance.
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Old 03-31-2015, 11:06 PM   #2
Laquais
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Doc:
http://cran.r-project.org/web/packag...IDR/RAPIDR.pdf
http://cran.r-project.org/web/packag...r-vignette.pdf
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Old 02-23-2016, 10:08 PM   #3
Manonathan
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Default Rapidr

Hi Laquais,
Have you tried RAPIDR?
I have some doubts regarding the the data 'outcomes'
Thanks in advance.
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Old 02-23-2016, 11:07 PM   #4
Laquais
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Hey Manonathan,

Yes, I integrated RAPIDR in a pipeline and I compared its results with a homemade pipeline. The results were convincing.
Today, the RAPIDR pipeline is used routinely to detect T21, T18, T13. Last I noticed, the results are reliable (I have now a new job but I continue to discuss with my old colleagues).

What are your doubts ?

Best regards.
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Old 02-23-2016, 11:26 PM   #5
Manonathan
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Hi Laquais,

Thanks for your reply.
I have finished makeBinnedCountsFile(c("file1.bam", "file2.bam"), c("sample1", "sample2"), 'output.fname',mask=NULL, k = 20000)
I got an output file 'output.fname'.
file1.bam and file2.bam are two bam files corresponding to aneuploidy samples.
I don't understand 'outcomes' dataframe.
I couldn't run createReferenceSetFromCounts('87.fname','a',method='zscore',gcCorrect = FALSE,gcContentFile = 'gcContent.fname')

I am getting error like this
"Loading binned counts file
Checking every sampleID has an outcome
Error in outcomes$SampleID : $ operator is invalid for atomic vectors"

Thanks and Regards,
Manonathan
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Old 02-24-2016, 07:36 AM   #6
Laquais
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RAPIDR transforms bam files into binned counts files to compare binned counts files with a reference set.


Reference set

That's why you have to gather some diploidy samples (more you have better is) and to use makeBinnedCountsFile with all your samples of the reference set. You can also add some aneuploidy samples (optionnal) in your reference set to have positive samples in your reference set (that's why you have a column Dx in outcomes). makeBinnedCountsFile with all your samples of the reference set will create an referenceSet.fname that you will use with createReferenceSetFromCounts.
You have to make an outcomes dataframe to define what is the sexe of the sample and if the sample is an aneuploidy sample (RAPIDR uses outcomes to calculate its zscores).
I advise you to create a file outcomes.txt and convert it in a dataframe with a R script.


Unknown samples

After that, you use makeBinnedCountsFile with your unknown samples (you don't know if these samples are diploide or not) to create unknown.fname
You use testUnknowns(ref.set, unknown.fname) to have the results.


"Error in outcomes$SampleID : $ operator is invalid for atomic vectors"
==> I think your column sampleID of outcomes is wrong. The SampleID must match with the sampleId you wrote in makeBinnedCountsFile

If you have :
makeBinnedCountsFile(c("file1.bam", "file2.bam",...), c("sample1", "sample2",...), 'reference.fname')

outcomes must be :
SampleID Dx Gender
1 sample1 Normal Female
2 sample2 Normal Female
3 sample3 T21 Female
......
......


I hope I am understable... My english is not very good. ^^
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Old 02-25-2016, 10:04 PM   #7
Manonathan
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Default Rapidr

Hi Laquais,

Thanks for your reply.
Now I got some idea about how to proceed with this package.
Thanks a lot. I have been struggling since December'15 to get output.
Thanks and Regards,
Manonathan
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Old 02-25-2016, 11:02 PM   #8
Laquais
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You're welcome,

I hope you will manage to obtain your results

Best regards.
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Old 05-08-2016, 06:35 PM   #9
WinterLi
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HI Manonathan,
I am using the RAPIDR, could you send me your complete scripts to perform it ?, from bam files to get the output ..... I am a new guy about NIPT
My email is : yogurt5276@dlmu.edu.cn
Thank you very much!!
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Old 11-21-2017, 12:04 PM   #10
PandoraMid
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Hi, I know that this is an old post, but I really need your help! I'm trying to use RAPIDR, but I have some problems with the reference creation. I explained my problems here: http://seqanswers.com/forums/showthr...ghlight=rapidr, can you help me? It is very important, I don't found anything on the web!
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