Closed rajeha closed 1 year ago
@rajeha This calculates the segment count (from your input) for each chromosome, then times it with 1e6/chromosome_size
to scale to per MB. So the result value is comparable between chromosomes.
In summary, for each chromosome:
segments x (1 x 10^6) / (chromosome size)
Code implementation is at https://github.com/ShixiangWang/sigminer/blob/95958d14821f862c52e7141daba17c2ba20daf7d/R/show_cn_distribution.R#L118
If you would not like to do this, set scale_chr
to FALSE
to get raw counts.
https://shixiangwang.github.io/sigminer/reference/show_cn_distribution.html
Got it, thanks!
Hi @ShixiangWang,
Thanks for all the quick responses to my questions on this package. Regarding the
show_cn_distribution(mode='cd')
function, would you please clarify the y-axis? What is the normalized count? Is it the number of copy number segments per chromosome? In that case, would it show more counts if a chromosome had several small CN segments as opposed to one large continuous segment?Thanks again!