Table 2 Notation for hrp2/3 deletion detection model

i

Sample index

i ∈ {1, 2, . . . , n}

j

Target gene index

j ∈ {1, 2, . . . , m}

X_n×m

Read count matrix

\({x}_{ij}\in {{\mathbb{Z}}}^{+}\)

C_n×m

Copy-number matrix

c_ij ∈ {0, 1}

δ

Indices of negative control samples

δ ⊂ {1, 2, . . . , n}

ϕ

Indices of target genes without known deletions (i.e., non-hrp)

ϕ ⊂ {1, 2, . . . , m}

a_n

Sample abundances

a_i ∈ [0, 1]

ϵ

Read misclassification / contamination rate

ϵ ∈ [0, 1]

ν

Read count overdispersion term

\(\nu \in {\mathbb{R}}+\)

p_ij

Unadjusted library proportion of sample i and target j

p_ij ∈ [0, 1]

π_ij

Adjusted library proportion of sample i and target j

π_ij ∈ [0, 1]