A dataset containing RCN data for the TCGA-AJ-A3EJ-01A-11D-A19X-01 sample
Usage
data(sample_data)Format
A data frame with 646 rows and 6 variables:
- Sample
sample name
- Chromosome
chromosome, 1:24
- Start
start position of segment
- End
end position of segment
- Num_Probes
number of probes
- Segment_Mean
log2 of the relative copy number
Examples
if (FALSE) {
data(sample_data)
sa = sample_data
sample_name = sa$Sample[1]
r = 2^sa$Segment_Mean
w = sa$End - sa$Start # should be +1
#
# RCN profile plot
plot_profile(sa, r, paste0(sample_name, '_RCN.tiff'),
ylim = c(0,5), ylab = 'RCN')
# ACN profile for CNH
grid = make_grid(purity = seq(0.2, 1, 0.01), ploidy = seq(1.5, 5, 0.01))
cnh = find_cnhplus(grid, r = r, w = w, k=2, plus = F)
# cnh
# purity ploidy kappa
#1 0.24 2.87 0.1384375
#2 0.27 3.86 0.1387208
#
acn_cnh = r2q(r, cnh$purity[1], cnh$ploidy[1])
plot_profile(sa, acn_cnh, paste0(sample_name, '_ACN_for_CNH.tiff'),
ylim = c(-10,10), ylab = 'ACN for CNH')
# ACN profile for CNH+
cnh_plus = find_cnhplus(grid, r = r, w = w, k=2, plus = T)
cnh_plus
# purity ploidy kappa
#1 1 4.98 0.1647427
#2 1 4.97 0.1648025
acn_cnhplus = r2q(r, cnh_plus$purity[1], cnh_plus$ploidy[1])
plot_profile(sa, acn_cnhplus, paste0(sample_name, '_ACN_for_CNHplus.tiff'),
ylim = c(0,10), ylab = 'ACN for CNH+')
}