data-raw/CN-features.R

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

# Concepts:
#
# Profile:
# Feature:
# Component:

## code to prepare `CN.features` dataset goes here
#
# BP10MB: 0、1、2、3、4、5、>5
# BPArm: 0、1、2、3、4、5、6、7、8、9、10、>10<=20、>20<=30、>30
# CN: 0、1、2、3、4、>4<=8、>8
# CNCP: 0、1、2、3、4、>4<=8、>8
# OsCN: 0、1、2、3、4、>4<=10、>10
# (log10 based)SegSize: <=2、>2<=3、>3<=4、>4<=5、>5<=6、>6<=7、>7<=8, >8
# BoChr: 1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20、21、22、23（remove Y, 23 means X）
# NChrV: <=5, >5<=10, >10<=15, >15<=20, >20 # this info can be reflected by NC50 and BoChr
# NC50: <=2, 3, 4, 5, 6, 7, >7
#
# Length of chains of oscillating copy-number (OsCN)
# Copy number change point (CNCP)
# SegSize (SS)
# Burden of Chromosome (BoChr)
# Number of Chromosome with 50% variation events (NC50)

features <- c("BP10MB", "BPArm", "CN", "CNCP", "OsCN", "SS", "NC50", "BoChr")

# Define two datasets, the one is for the default situation, the other collects all features can be used.

# When component is a unique value, min=max
# When component is a data range, make left open and right closed
CN.features <- dplyr::tibble(
  feature = features[c(rep(1, 7), rep(2, 14), rep(3, 7), rep(4, 7), rep(5, 7), rep(6, 8), rep(7, 7), rep(8, 23))],
  min = c(
    c(0:5, 5),
    c(0:10, 10, 20, 30),
    c(0:4, 4, 8),
    c(0:4, 4, 8),
    c(0:4, 4, 10),
    c(-Inf, 2:8),
    c(-Inf, 3:7, 7),
    c(1:23)
  ),
  max = c(
    c(0:5, Inf),
    c(0:10, 20, 30, Inf),
    c(0:4, 8, Inf),
    c(0:4, 8, Inf),
    c(0:4, 10, Inf),
    c(2:8, Inf),
    c(2:7, Inf),
    c(1:23)
  )
)


CN.features <- get_feature_components(CN.features)

usethis::use_data(CN.features, overwrite = TRUE)