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gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
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CNV estimation for WES data using TitanCNA #90

Open asaki1986 opened 3 years ago

asaki1986 commented 3 years ago

Hi,

Thanks for providing the TitanCNA tool to evaluate the CNV status of samples.

However, I am quite confusing about the output of the titan result, especially the copy number (log ratio) displayed in the CNV plot.

Result obtained in XXXXX_cluster2.titan.txt showed neutral status (copy number = 2) across the chromosomes of the sample, but was set to 1 (Copy Number (log ratio)) in the CNV plot.

Can anyone explain the algorithm to calculate the Copy Number (log ratio)? Which column of data ( XXXXX_cluster2.titan.txt) was used to plot the CNV?

image

Chr Position RefCount Depth AllelicRatio LogRatio CopyNumber TITANstate TITANcall ClonalCluster CellularPrevalence Subclone1.CopyNumber Subclone1.TITANcall Subclone1.Prevalence logR_Copy_Number Corrected_logR Corrected_Ratio Corrected_Copy_Number Corrected_Call 1 871334 60 60 1 0.128473804031386 2 3 HET NA NA 2 HET 1 4.2739032317698 0.128574762140231 1 2 NEUT 1 884101 10 40 0.25 0.128473804031386 2 3 HET NA NA 2 HET 1 4.2739032317698 0.128574762140231 0.249812167512054 2 NEUT 1 896271 48 48 1 0.128473804031386 2 3 HET NA NA 2 HET 1 4.2739032317698 0.128574762140231 1 2 NEUT 1 898852 0 206 0 0.128473804031386 2 3 HET NA NA 2 HET 1 4.2739032317698 0.128574762140231 0 2 NEUT 1 1372668 159 159 1 -0.0474000036519164 2 3 HET NA NA 2 HET 1 3.78302391790213 -0.0474395834741863 1 2 NEUT 1 1386016 34 74 0.459459459459459 -0.0474000036519164 2 3 HET NA NA 2 HET 1 3.78302391790213 -0.0474395834741863 0.45942504778268 2 NEUT 1 1386408 6 10 0.6 -0.0474000036519164 2 3 HET NA NA 2 HET 1 3.78302391790213 -0.0474395834741863 0.600084882136057 2 NEUT 1 1396238 217 217 1 -0.0474000036519164 2 3 HET NA NA 2 HET 1 3.78302391790213 -0.0474395834741863 1 2 NEUT 1 1846765 2 79 0.0253164556962025 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 0.0248728317773528 4 AMP 1 1847979 124 125 0.992 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 0.992459807319409 4 AMP 1 1848160 177 177 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1849529 4 146 0.0273972602739726 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 0.0269555810079178 4 AMP 1 1849530 147 147 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1849744 175 175 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1853863 63 63 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1853921 55 55 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1854546 187 187 1 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.186277832379926 1 4 AMP 1 1854717 69 71 0.971830985915493 -0.186114656916182 4 8 BCNA 1 1 4 BCNA 1 3.43593239116493 -0.18627783

Thanks, Junfeng