Table 1 Summary of functions to extract built-in data
Function name | Function |
|---|---|
get_tpm(cancer) | Extract the TPM matrix of a specific type of cancer in TCGA. eg, get_tpm("COAD") |
get_paired_tpm(cancer) | Extract the TPM matrix of a specific type of cancer with paired samples (n > 20) in TCGA. eg, get_paired_tpm("COAD") |
get_meta(cancer) | Extract the clinical information of a specific type of cancer in TCGA. eg, get_meta("COAD") |
get_tmb() | Extract the TMB matrix of all samples in TCGA |
get_msi() | Extract the MSI matrix of all samples in TCGA |
get_methy() | Print the link of the whole methylation matrix for users to download |
get_promoter_methy() | Extract promoter methylation of a specific type of tumor |
get_immu_ratio() | Extract the immune cell ratio of all samples in TCGA |
get_immuscore() | Extract the immune score of all samples in TCGA |
get_cancers() | Return the sample summary of 33 types of cancer in TCGA |
get_paired_cancers() | Return the sample summary of 15 types of cancer containing more than 20 paired samples in TCGA |