TCGA CNV data comes as CNV segments. Each segment has a value, called segment mean. These values are continuous values. However biologist often refer copy number as gain and loss, discrete states. I am interested in the distribution of segment means for TCGA pan-cancer cohort, as well as individual TCGA cohort. The distribution will help me to determine the cutoff for determine copy number gain or loss.
In a diploid genome, a single-copy gain in a perfectly pure, homogeneous sample has a copy ratio of 3/2. In log2 scale, this is log2(3/2) = 0.585, and a single-copy loss is log2(1/2) = -1.0.” However, most tumors are heterogeneous (clonal tumor populations) and have some normal stroma. Therefore, the sample’s purity need to be considered so alterations are not missed.
- generate copy number segment mean distribution without adjust for purity
- generate copy number adjusted segment mean (adjusted for purity) distribution .
TCGA CNV data comes as CNV segments. Each segment has a value, called segment mean. These values are continuous values. However biologist often refer copy number as gain and loss, discrete states. I am interested in the distribution of segment means for TCGA pan-cancer cohort, as well as individual TCGA cohort. The distribution will help me to determine the cutoff for determine copy number gain or loss.
In a diploid genome, a single-copy gain in a perfectly pure, homogeneous sample has a copy ratio of 3/2. In log2 scale, this is log2(3/2) = 0.585, and a single-copy loss is log2(1/2) = -1.0.” However, most tumors are heterogeneous (clonal tumor populations) and have some normal stroma. Therefore, the sample’s purity need to be considered so alterations are not missed.