This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why I'm not getting KM plots at a significant p-value?

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)
<h5>KM Analysis</h5>
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
km os plot rna-seq

0 answers

No answers yet.

Log in to answer this question.