Entering edit mode
18 months ago
prithvi.mastermind
▴
50
I'm interested in plotting KM plot for assessing the OS. But while plotting I'm not getting any value significant (p-value < 0.05). Is my code correct?
<h5>Load packages</h5>library(survival)
library(survminer)
library(dplyr)
library(survMisc)
library(GGally)
library(survcomp)
library(RegParallel)
JMS <- read.delim(file = "LUAD_SURVIVAL.txt")
JMS = JMS %>% mutate(group = case_when(TDRKH> quantile(TDRKH, 0.5) ~ 'TDRKH(High)', TDRKH < quantile(TDRKH, 0.5) ~ 'TDRKH(Low)', TRUE ~ NA_character_ ))
fit <- survfit(Surv(Time, Status) ~ group, data = JMS)
ggsurvplot(fit, pval = TRUE, conf.int = TRUE, conf.int.style = "step", risk.table = TRUE, risk.table.col = "strata", break.time.by = 1000, linetype = "strata", surv.median.line = "hv", ggtheme = theme_bw(),palette = c("#E7B800", "#2E9FDF"))
My Data in LUAD_SURVIVAL.txt is:
Sample Status Time LRRK2 SNCA TDRKH
TCGA.38.4625.01A 0 2973 -0.383829368 -0.219402428 0.6500694
TCGA.38.4627.01A 1 1147 -1.45793859 -0.022231288 -0.5830916
TCGA.38.4632.01A 1 1357 -1.316342217 -0.162383739 1.146363
TCGA.44.2655.01A 0 1324 0.046189981 -0.773276551 2.024474
TCGA.44.2657.01A 0 1351 -0.975033238 -0.256492538 0.171917
TCGA.44.2661.01A 0 1159 -0.78239234 0.327366323 0.1126025
TCGA.44.2662.01A 0 1280 -0.758485389 -1.437559471 1.273534
TCGA.44.2665.01A 0 1301 -0.999667232 -0.440681708 0.009561531
TCGA.44.2668.01A 1 761 -0.644422547 -1.445774753 0.9272611
TCGA.44.3396.01A 0 1130 -1.245042532 -0.395511449 -0.1383681
TCGA.44.6145.01A 0 595 -0.200550603 -1.307112908 1.290406
TCGA.44.6147.01A 0 845 -0.297408216 -0.358287055 0.6861114
TCGA.44.6776.01A 0 2616 0.668204053 -1.045513127 0.3604824
TCGA.44.6777.01A 1 987 0.774933934 0.120296574 1.095746
TCGA.44.6778.01A 0 1864 0.395187563 0.209133034 0.2749578
TCGA.49.4490.01A 1 385 -1.751088203 -1.655575684 0.03521947
TCGA.49.4512.01A 1 905 0.332495541 -0.456119236 1.154696
TCGA.49.6743.01A 0 1621 -0.641826568 -0.79901757 1.403125
TCGA.49.6744.01A 0 1683 -0.403411305 0.006217842 0.300926
TCGA.49.6745.01A 0 522 0.046500089 -0.621497979 0.228453
TCGA.49.6761.01A 0 354 -0.857810394 -2.056883586 1.437622
TCGA.50.5930.01A 1 282 -0.87400339 0.093055616 1.570507
TCGA.50.5931.01A 1 434 -2.277003104 -0.995236158 0.3775715
TCGA.50.5932.01A 1 1235 -0.475064449 -2.294646772 1.211618
TCGA.50.5933.01A 1 2393 -0.635493519 -0.647664896 1.576859
TCGA.50.5935.01A 1 653 0.144475137 -1.286987274 2.029953
TCGA.50.5939.01A 1 460 -0.217287921 -0.297524684 -0.1612658
TCGA.50.6595.01A 1 189 -2.074430113 -1.31726386 -1.05404
TCGA.55.6968.01A 1 1293 -1.510117962 -0.110645011 1.025638
TCGA.55.6970.01A 1 464 0.493536516 -0.785224767 0.8346801
TCGA.55.6971.01A 0 1400 0.208688847 -0.399653744 0.9952134
TCGA.55.6972.01A 1 1632 -1.125136651 -2.586160697 1.663106
TCGA.55.6975.01A 1 118 -2.092639366 -0.831491754 -0.08286432
TCGA.55.6978.01A 1 176 -1.239634382 -0.579709271 -0.248721
TCGA.55.6979.01A 1 237 -0.591083585 -0.795370819 0.4372139
TCGA.55.6980.01A 0 2109 -0.752056711 -0.697417076 0.7107928
TCGA.55.6981.01A 1 1379 -1.439636573 -1.162752821 0.7467579
TCGA.55.6982.01A 1 995 -0.559143952 -0.923362752 0.2045792
TCGA.55.6984.01A 1 760 -0.991059081 -2.752376513 -0.6147963
TCGA.55.6985.01A 0 1233 -0.503782815 -0.359211612 0.2640623
TCGA.55.6986.01A 0 3261 -0.057757299 -0.395037493 0.161682
TCGA.73.4676.01A 1 281 -0.938051892 -1.009113608 1.945119
TCGA.91.6828.01A 0 323 -0.246057181 -0.825642817 1.327468
TCGA.91.6829.01A 1 1258 -1.300016577 0.383268015 1.390523
TCGA.91.6831.01A 0 310 -1.5698444 -1.168399177 0.8284916
TCGA.91.6835.01A 0 79 -0.651069358 -0.390002878 1.839444
TCGA.91.6836.01A 0 417 -1.78515033 -1.364946704 3.60664
TCGA.91.6847.01A 0 842 -3.538866094 -0.87741001 0.9409349
TCGA.91.6849.01A 0 35 -0.202941284 0.13610892 1.131687
