Question: ASCAT input files
0
gravatar for lmarruda
3.7 years ago by
lmarruda0
lmarruda0 wrote:

I am trying to build input matrices of LogR and B Allele Frequency (BAF) data (ASCAT). I have copy number files and allelic frequencies files

Table 1:

feature chromosome start end segments

1:840001-870000 1 840001 870000 -0.003

Table 2: Chrom Pos VAF

1 876499 1.0000000

1 878314 0.6666667

How to pair table 2 into the copy number intervals of table 1? Have tried this, but does not work:

for (i in 1:nrow(testcna)) { testX <- which(testcna$chromosome == testbaf$Chrom[i] & (testcna$start <= testbaf$Pos[i] & testcna$end >= testbaf$Pos[i]))
}

sequencing • 1.4k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by lmarruda0

Just for clarification so that I maybe can answer your question, what is your goal? To prepare the LogR and BAF-files so that you can run ASCAT to get copy number profiles of your sample? Or have you already run ASCAT?

ADD REPLYlink written 3.7 years ago by cbst150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1433 users visited in the last hour