Curated colorectal cancer clinical data — clin

Clinical information for colorectal cancer samples assembled from public repositories: the GEO datasets GSE14333, GSE17538, GSE18088, GSE26906, GSE31595, GSE33113, GSE37892, GSE39084, and GSE39582 (the PETACC-3 cohort), and TCGA colon and rectal cancer clinical exports. The data contain research-level variables only and no patient identifiers. These objects are carried over from the archived curatedClinicalData repository without changing the stored values.

Usage

clin_crc

clin_crc_gf

clin_crc_cell

Format

A data frame with 25 columns:

sample: Sample or patient identifier.
sex: Sex ("M"/"F").
age: Age at diagnosis in years.
tnm.stage: TNM stage as an ordered number.
tnm.t, tnm.n, tnm.m: TNM T, N, and M categories.
lymphnodes: Lymph node involvement.
tumor.location: Tumour location ("L"/"R").
grade: Tumour grade.
chemotherapy.adjuvant: Adjuvant chemotherapy indicator.
rfs.event, rfs.delay: Relapse-free survival event and time (years).
os.event, os.delay: Overall survival event and time (years).
dfs.event, dfs.delay: Disease-free survival event and time (years).
mmr.status, cimp.status, cin.status: Molecular subtype indicators.
tp53.mutation, kras.mutation, braf.mutation: Mutation status.
dataset: Source dataset.
cms: Consensus molecular subtype label.

A data frame with 2,868 rows and 25 columns, in the same layout as clin_crc. This version adds the TCGA update of 2018.

A data frame with 2,865 rows and 25 columns, in the same layout as clin_crc. This version carries the 2019 TCGA cell-line update.

Source

GEO series GSE14333, GSE17538, GSE18088, GSE26906, GSE31595, GSE33113, GSE37892, GSE39084, and GSE39582; TCGA clinical exports.

Examples

dim(clin_crc)
#> [1] 2816   25
table(clin_crc$dataset)
#> 
#> GSE14333 GSE17538 GSE18088 GSE26906 GSE31595 GSE33113 GSE37892 GSE39084 
#>      290      232       53       90       37       90      130       68 
#> GSE39582  PETACC3     TCGA 
#>      566      688      572