construct_PhenoData: construct Phenotype data frame
In ShixiangWang/iProfile: integrated cancer Profile using multiple datasets

Description Usage Arguments Details Value Author(s) See Also

This function is used to construct a Phenotype data.frame for ExpressionSet object

construct_PhenoData(Study_ID = NULL, Sample_ID = NULL, Platform = NULL,
  Type = NULL, Gender = NA, Age = NA, Tumor_stage = NA,
  Family_history = NA, Smoking_status = NA, Tumor_feature = NA,
  Mutation_status = NA, Survival_status = NA, Survival_time = NA,
  Preprocessed_Method = "RMA", Matched_CNV_ID = NA,
  Tumor_Normal_Matched_ID = NA)

`Study_ID`	a character. Set a ID for a study, like GSEXXXXX for GEO study.
`Sample_ID`	a character. Set a ID for a sample, like GSMXXXXX for GEO samples.
`Platform`	a character. Set platform for study. if it is `NULL`, `annotation` function will be used to get the platform. It is ok to use annotation platform like org.Hs.eg.db
`Type`	a character. Column name of `pData`. It is used to tell the tissue type, such as Normal, LUAD ..
`Gender`	a character. Column name of `pData`. It is used to identify where the Gender column are.
`Age`	like above.
`Tumor_stage`	like above.
`Family_history`	like above.
`Smoking_status`	like above.
`Tumor_feature`	like above. You can get what you think related to feature but not set in other argument.
`Mutation_status`	like above.
`Survival_status`	like above.
`Survival_time`	like above.
`Preprocessed_Method`	a character used to set what method used to preprocess raw data.
`Matched_CNV_ID`	used to label sample ID which has paired CNV data
`Tumor_Normal_Matched_ID`	used to label sample ID which is Tumor and Normal tissue matched.

Although ExpressionSet object has a regular pattern for phenotype data, but diverse in different studies. So if we want to merge data from different studies, we have to uniform all variable names of phenotype data . This function is for this purpose and mainly used by create_Exprset. User can use this function to create phenodata separately.

a data.frame

Shixiang Wang <w_shixiang@163.com>

ExpressionSet

ShixiangWang/iProfile documentation built on May 11, 2019, 6:25 p.m.