From 6873f6b4e7b5c59eb12992ba9e8a4c1678a68199 Mon Sep 17 00:00:00 2001 From: Jeffrey Jiang Date: Sat, 15 Jan 2022 11:49:57 -0600 Subject: [PATCH] Updated comments for readability --- src/penalty_selection.py | 3 ++- src/postprocess.R | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/penalty_selection.py b/src/penalty_selection.py index c3e2125..4d3f213 100644 --- a/src/penalty_selection.py +++ b/src/penalty_selection.py @@ -9,9 +9,10 @@ #------------------------------------------------------------# # The automated lambda selection pipeline is as follows: -# 1) Run CliP with 11 different lambda: [0.01, 0.03, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, 0.2, 0.225, 0.25]. +# 1) Run CliP with 11 different lambdas: [0.01, 0.03, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, 0.2, 0.225, 0.25]. # 2) For each sample, compute a score: A = |(max(CP)−purity)/purity|. # If there are one or more results that satisfy A < 0.01, we select the largest lambda associated with those results. +# (We observed A<0.01 in more than 70% of the PCAWG samples) # If all scores A are greater than 0.01, we choose the lambda associated with the smallest A. #------------------------------------------------------------# diff --git a/src/postprocess.R b/src/postprocess.R index 5d35186..953ac45 100755 --- a/src/postprocess.R +++ b/src/postprocess.R @@ -39,6 +39,7 @@ least.ratio <- 0.05 SAFETY <- 0.05 N.REP <- 30 RATIO.TH <- 0.90 +# The 11 lambda values in the default lambda list Lambda_list = c(0.01, 0.03, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, 0.2, 0.225, 0.25) if(!dir.exists(output.prefix)){