diff --git a/analyses/braf-fusions/03-survival-by-braf-breakpoints.html b/analyses/braf-fusions/03-survival-by-braf-breakpoints.html index 7ce3979d..daed5ef9 100644 --- a/analyses/braf-fusions/03-survival-by-braf-breakpoints.html +++ b/analyses/braf-fusions/03-survival-by-braf-breakpoints.html @@ -431,12 +431,12 @@
Load libraries and set directories
library(data.table)
library(tidyverse)
-## ── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.2 ──
+## ── Attaching packages ─────────────────────────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.4.0 ✔ purrr 1.0.1
## ✔ tibble 3.1.8 ✔ dplyr 1.1.0
## ✔ tidyr 1.3.0 ✔ stringr 1.5.0
## ✔ readr 2.1.3 ✔ forcats 1.0.0
-## ── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+## ── Conflicts ────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::between() masks data.table::between()
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::first() masks data.table::first()
@@ -469,7 +469,7 @@ 2024
columns
braf_hist <- read_tsv(hist_file)
## Rows: 172 Columns: 48
-## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (29): Kids_First_Biospecimen_ID_normal, predicted_ancestry, Kids_First_P...
## dbl (18): EAS_prob, AFR_prob, AMR_prob, SAS_prob, EUR_prob, PC1, PC2, PC3, P...
@@ -511,7 +511,7 @@ 2024
title = "LGG, BRAF fusion")
km_plot_type
-
+
ggsave(file.path(plot_dir, "pbta_ancestry_km_efs_breakpoint_type.pdf"),
width = 7.5, height = 5)
Run Kaplan-Meier analysis of event-free survival by breakpoint
@@ -531,7 +531,7 @@
2024
title = "LGG, BRAF fusion")
km_plot_group
-
+
ggsave(file.path(plot_dir, "pbta_ancestry_km_efs_breakpoint_group.pdf"),
width = 7.5, height = 5)
Run Kaplan-Meier analysis of event-free survival by predicted
@@ -551,7 +551,7 @@
2024
title = "LGG, BRAF fusion, breakpoint 16:09")
km_plot_group
-
+
ggsave(file.path(plot_dir, "pbta_ancestry_km_efs_16_9_predicted_ancestry.pdf"),
width = 7.5, height = 5)
Run Kaplan-Meier analysis of event-free survival by predicted @@ -571,7 +571,7 @@
ggsave(file.path(plot_dir, "pbta_ancestry_km_efs_15_9_predicted_ancestry.pdf"),
width = 7.5, height = 5)
Run and plot cox proportional hazards model of EFS including tumor
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint15_9_resection_ancestry.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint15_9_resection_ancestry.pdf
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diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_group.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_group.pdf
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diff --git a/analyses/braf-fusions/plots/pbta_ancestry_km_efs_15_9_predicted_ancestry.pdf b/analyses/braf-fusions/plots/pbta_ancestry_km_efs_15_9_predicted_ancestry.pdf
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diff --git a/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_type.RDS b/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_type.RDS
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diff --git a/analyses/survival/01-prepare-survival.nb.html b/analyses/survival/01-prepare-survival.nb.html
index 71816ea9..1a65b791 100644
--- a/analyses/survival/01-prepare-survival.nb.html
+++ b/analyses/survival/01-prepare-survival.nb.html
@@ -1338,18 +1338,12 @@
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