stageParse: Parse TCGA clinical data patients tumor stage information

In FanZhang9/TCGAcm: TCGA clinical data mining

Description

Parse TCGA clinical data patients tumor stage information

Usage

stageParse(filenames, 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.

simplify

When simplify = FALSE, it will return the full detail of patient basic information (bcr_patient_barcode, etc.), and tumor stage. When simplify = TRUE, it will return When simplify = FALSE, the full information (including bcr_patient_barcode, bcr_patient_uuid, age_at_initial_pathologic_diagnosis, tumor_tissue_site, gender, race, stage_system_version, stage_clinical_stage, stage_pathologic_stage, stage_tnm_clinical_T, stage_tnm_clinical_N, stage_tnm_clinical_M, stage_tnm_pathologic_T, stage_tnm_pathologic_M, stage_tnm_pathologic_N, stage_psa_value, stage_days_to_psa, stage_gleason_gleason_score, stage_gleason_primary_pattern, stage_gleason_secondary_pattern, stage_gleason_tertiary_pattern, stage_ann_arbor_b_symptoms, stage_ann_arbor_extranodal_involvement, stage_serum_markers, stage_igcccg_stage, stage_masaoka_stage) When simplify = TRUE, it will only return the key tumor stage information (bcr_patient_barcode, bcr_patient_uuid, age_at_initial_pathologic_diagnosis, tumor_tissue_site, gender, race, stage_system_version, stage_pathologic_stage, stage_tnm_pathologic_T, stage_tnm_pathologic_M, stage_tnm_pathologic_N)

Value

A tibble with every TCGA clinical xml files patients basic information (barcode, gender, etc.) and tumor stage information.

Author(s)

Fan Zhang

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