I was wondering if there is a threshold I could use on the log-odds-ratio (MAF) value to call a region as LOH? I am calculating the converted MAF_R as sqrt(abs(MAF_R)). The real purpose is to make a copynumber frequency plot like this but with MAF values:
These plots need a threshold to calculate the frequency above it so just wondering if I can use the converted MAF_R value and then use a threshold to calculate the frequencies? But what threshold would it be for a region to be called as LOH.
I was thinking of using anything above 1 as LOH, but if I plot the converted MAF_R values across the genome and color it by LCN (which means LOH), there are some segments with MAF close to 0 and LCN = 0. Here's an example for a sample:
This is the profile generated by cnv_facets:
This is a segment plot I made just using the converted MAF values and colored by LCN
Hi,
I was wondering if there is a threshold I could use on the log-odds-ratio (MAF) value to call a region as LOH? I am calculating the converted MAF_R as
sqrt(abs(MAF_R)). The real purpose is to make a copynumber frequency plot like this but with MAF values:These plots need a threshold to calculate the frequency above it so just wondering if I can use the converted MAF_R value and then use a threshold to calculate the frequencies? But what threshold would it be for a region to be called as LOH.
I was thinking of using anything above 1 as LOH, but if I plot the converted MAF_R values across the genome and color it by LCN (which means LOH), there are some segments with MAF close to 0 and LCN = 0. Here's an example for a sample:
This is the profile generated by cnv_facets:
This is a segment plot I made just using the converted MAF values and colored by LCN
Any advice would be really helpful!
Thanks!