calc_1d_wgs function

Return mixture estimation for percentage of normal cells and tumor (1 normal + 1 tumor) with wgs data Takes baf, lrr, n_baf and nrc

calc_1d_wgs(baf, lrr, n_baf, nrc)

Arguments

• baf: a numeric vector. Each element is the mean adjusted B allele frequency for that segment, calculated as the mean of baf_tumor/baf_normal/2 for that segment
• lrr: a numeric vector. Each element is the log ratio of the tumor read count and the normal read count for a segment, defined as log(tumorCount/normalCount)
• n_baf: a numeric vector
• nrc: a numeric vector. Each element is the normal read count of the segment divided by two

Returns

• sol1: a numeric number. It provides the estimated percentages of normal from the best solution. The number is the percentage of the estimated normal percentage.

• sol2: a numeric number. It provides the estimated percentages of normal from the second best solution. The number is the percentage of the estimated normal percentage.