tc_geneset_comparison: Gene Set Comparison Function for TCGA Dataset

In cannin/tumorcomparer: Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Gene Set Comparison Function for TCGA Dataset

Description

Gene Set Comparison Function for TCGA Dataset

Usage

tc_geneset_comparison(
  gene_list,
  cancer_type = NULL,
  tcga_ids = NULL,
  cclp_ids = NULL,
  tc_dataset = NULL,
  tc_dataset_dir = NULL,
  remove_errored_dataset_comparisons = FALSE,
  remove_tmp_files = TRUE,
  run_mds = TRUE,
  verbose = FALSE
)

Arguments

gene_list	a vector of HGNC gene symbols which will be used to perform the comparison
cancer_type	TCGA cancer name (GBM, LGG, etc.)
tcga_ids	a vector of TCGA IDs for analysis; cannot be combined with cancer_type
cclp_ids	a vector of CCLP IDs for analysis; cannot be combined with cancer_type
tc_dataset	path to RData for TumorComparer dataset from publication; see details
tc_dataset_dir	path to directory with TumorComparer dataset as text files (recommended instead of tc_dataset); see details
remove_errored_dataset_comparisons	will skip the data types which can't be compared for technical reasons(no enaugh genes to compare, or data contain only 0 values) when set to TRUE (Default: FALSE)
remove_tmp_files	remove temporary files (Default: TRUE)
run_mds	a boolean, whether to run multidimensional scaling (MDS) on dataset (Default: TRUE)
verbose	show debugging information

Details

This function requires downloading: https://zenodo.org/record/4627644/files/tc_data_pancancer_march2021.tar.gz?download=1

The above data is the dataset used in the 2021 TumorComparer publication. Data can then be loaded from the extracted text files if 'tc_dataset_dir' parameter is provided or data can be loaded from an RData workspace variable using the 'tc_dataset' parameter if it has been pre-generated. tc_dataset_dir' is recommended.

Value

returns comparison list for specified genes. The output list is described in run_comparison_config_list function documentation

Note

FIXME ADD EXAMPLE

cannin/tumorcomparer documentation built on Feb. 7, 2023, 3:13 p.m.