create_Exprset: create an ExpressionSet object from matched ExpressionSets
In ShixiangWang/iProfile: integrated cancer Profile using multiple datasets

Description Usage Arguments Details Value Author(s) See Also

Auto-processing function for creating phenotype data and feature data for ExpressionSet object. An ExpressionSet object generated from two Expression lists Mat and Res.

create_Exprset(Mat = NULL, Res = NULL, id = NULL, keepSource = NULL,
  rev_nams = NULL, features = c("ID", "Gene.title", "Gene.symbol",
  "Gene.ID"), Study_ID = NULL, Platform = 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, ...)

`Mat`	an ExpressionSet object list. The list is used to store a list of `ExpressionSet` objects import from `GEOquery::getGEO` function which download and import Matrix Series Files.
`Res`	an ExpressionSet object list. The list is used to store a list of `ExpressionSet` objects preprocessed by `Oligo` or `affy` package and have only arrayData object. Due to any object in the list has no detail `pData` or `fData`, so we use this function to put `pData` and `fData` we need in `Mat` list to `Res` list.
`id`	a character. We use this parameter to label one object name in both `Mat` and `Res` list.
`keepSource`	a character. It marks a column name of pData of ExpressionSet object. Not always we want to keep all samples, so we can use this argument to filter samples we want to keep. For example, in cancer study, we want to keep some types of cancer or some histological type of one cancer etc..
`features`	a character vector. This paramter is used to keep `fData` variables.
`Study_ID`	a character. Set a ID for a study, like GSEXXXXX for GEO study.
`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
`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.
`Sample_ID`	a character. Set a ID for a sample, like GSMXXXXX for GEO samples. If not specified, it will be equal to `id` parameter.
`Type`	a character. Column name of `pData`. It is used to tell the tissue type, such as Normal, LUAD ..

This function is used to create an ExpressionSet object which pData and fData are automatically processed. Mat and Res are list of matched ExpressionSet object, id is used to identify which dataset in ExpressionSet list will be processed. Most of other arguments are used for constructing pData.

an ExpressionSet object

Shixiang Wang <w_shixiang@163.com>

ExpressionSet, construct_PhenoData

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