CorrectTNM: Version control for TCGA TNM stage

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

Version control for TCGA TNM stage

Usage

CorrectTNM(data, version = "stageVesion", toVersion = 8,
  T.status = "pT", N.status = "pN", M.status = "M.status",
  Np.counts = "Np.count", correctFile = NULL)

Arguments

data	design object
version	the colname of AJCC stage version.Note that the element of version should be "6th" like.
toVersion	the final version you want to change.
T.status	the colnames of T stage
N.status	the colnames of N stage
M.status	the colnames of M stage
Np.counts	the colnames of positive lymph nodes
correctFile	the path of reference database.Default = system.file("extdata", "STAD_AJCC stage.xlsx", package = "lucky").It supports self-defined dataset with same format.

Details

The most part of correction is the data from correctFile. It should be kept latest.
For gastric cancer,before 5th(including 4th),the nodal involvement is classified into pN0, pN1, and pN2, based on the site of the metastasis in relation to the primary tumor.Afterwards,the number of positive lymph nodes become the details to stage N.

Value

a data frame

Author(s)

Weibin Huang<[e-mail]>

See Also

UICC 4th

Examples

## get your design data
load("E:/RCloud/database/DataDownload/TCGA-TCGABiolinks/STAD_Download/2018-12-3/design_STAD.rda")
colnames(design)
data = design
## update the TNM stage to 8th version
data2 <- CorrectTNM(data,
                    version = "stageVesion",
                    toVersion = 8,
                    T.status = "pT",
                    Np.counts = "Np.count",
                    M.status = "M.status")

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.