tumor_eventParse: Title Parse TCGA clinical tumor event data from XML files

In FanZhang9/TCGAcm: TCGA clinical data mining

Description

Title Parse TCGA clinical tumor event data from XML files

Usage

tumor_eventParse(filenames, dir = ".", simplify = TRUE)

Arguments

filenames	A vector contain the names of TCGA clinical XML files directorys and names (tcga_files_path/xml_file_names), which can easily retrieve by 'list.files(path = ".", pattern = "*.xml",recursive = TRUE)'. The working directorys is the key, please check the names (which contain tcga_files_path/XML_file_names) is correct.
dir	file directory contained the XML files, default is current directory "." tumor_eventParse() will extract the TCGA xml files, as you frome the follow up record of XML files. Some patient may have multiple record of tumor event, others have none or When simplify = TRUE, the returned tibble will contain column as following (bcr_patient_barcode, bcr_patient_uuid, age_at_initial_pathologic_diagnosis, tumor_tissue_site, gender, stage_event_system_version, stage_pathologic_stage, new_tumor_event_list). last 3 column (new_tumor_neoplasm_event_type, new_tumor_occurrence_anatomic_site, new_neoplasm_event_type), is a list in a tibble column, due to one patient often have several new tumor metastasis event. When simplify = FALSE, the returned tibble will contain bcr_patient_barcode, bcr_patient_uuid, age_at_initial_pathologic_diagnosis, tumor_tissue_site, gender, stage_event_system_version, stage_pathologic_stage, new_tumor_event_list. The last one new_tumor_event_list is the full tumor event data, store in the tibble column, and each element is a table
simplify	When simplify = TRUE, it will return the patients basic ID information, new_tumor_neoplasm_event_type, new_tumor_occurrence_anatomic_site, new_neoplasm_event_type. When simplify = FALSE, it will return the patients basic ID information, and a tibble column, new_tumor_event_list, contain all the tumor event of the patient.

Value

a tibble with tumor event data

Author(s)

Fan Zhang

See Also

the vitalParse function for extract the vital data, also have the days to new tumor event, which can be used for PFS analysis. link{vitalParse}

FanZhang9/TCGAcm documentation built on Dec. 17, 2021, 8:23 p.m.