Fetch Identifier Value from Pan-cancer Dataset

Identifier includes gene/probe etc.

Usage

get_ccle_cn_value(identifier)

get_ccle_gene_value(identifier, norm = c("rpkm", "nc"))

get_ccle_protein_value(identifier)

get_ccle_mutation_status(identifier)

get_pancan_value(
  identifier,
  subtype = NULL,
  dataset = NULL,
  host = available_hosts(),
  samples = NULL,
  ...
)

get_pancan_gene_value(identifier, norm = c("tpm", "fpkm", "nc"))

get_pancan_transcript_value(identifier, norm = c("tpm", "fpkm", "isopct"))

get_pancan_protein_value(identifier)

get_pancan_mutation_status(identifier)

get_pancan_cn_value(identifier, gistic2 = TRUE, use_thresholded_data = FALSE)

get_pancan_methylation_value(
  identifier,
  type = c("450K", "27K"),
  rule_out = NULL,
  aggr = c("NA", "mean", "Q0", "Q25", "Q50", "Q75", "Q100")
)

get_pancan_miRNA_value(identifier)

get_pcawg_gene_value(identifier)

get_pcawg_fusion_value(identifier)

get_pcawg_promoter_value(identifier, type = c("raw", "relative", "outlier"))

get_pcawg_miRNA_value(identifier, norm = c("TMM", "UQ"))

get_pcawg_APOBEC_mutagenesis_value(
  identifier = c("tCa_MutLoad_MinEstimate", "APOBECtCa_enrich", "A3A_or_A3B",
    "APOBEC_tCa_enrich_quartile", "APOBECrtCa_enrich", "APOBECytCa_enrich",
    "APOBECytCa_enrich-APOBECrtCa_enrich", "BH_Fisher_p-value_tCa", "ntca+tgan",
    "rtCa_to_G+rtCa_to_T", "rtca+tgay", "tCa_to_G+tCa_to_T",
    "ytCa_rtCa_BH_Fisher_p-value", "ytCa_rtCa_Fisher_p-value", "ytCa_to_G+ytCa_to_T",
    "ytca+tgar")
)

Arguments

identifier

a length-1 character representing a gene symbol, ensembl gene id, or probe id. Gene symbol is highly recommended.

norm

the normalization method.

subtype

a length-1 chracter representing a regular expression for matching DataSubtype column of UCSCXenaTools::XenaData.

dataset

a length-1 chracter representing a regular expression for matching XenaDatasets of UCSCXenaTools::XenaData.

host

a character vector representing host name(s), e.g. "toilHub".

samples

a character vector representing samples want to be returned.

...

other parameters.

gistic2

if TRUE (default), use GISTIC2 data.

use_thresholded_data

if TRUE, use GISTIC2-thresholded value.

type

methylation type, one of "450K" and "27K". for function get_pcawg_promoter_value, it can be one of "raw", "relative", "outlier".

rule_out

methylation sites to rule out before analyzing.

aggr

apporaches to aggregate the methylation data, default is 'NA', in such case, a mean value is obtained for gene-level methylation. Allowed value is one of c("NA", "mean", "Q0", "Q25", "Q50", "Q75", "Q100"). Here, Q50 is median.

Value

a named vector or list.

Functions

• get_ccle_cn_value(): Fetch copy number value from CCLE dataset

• get_ccle_gene_value(): Fetch gene expression value from CCLE dataset

• get_ccle_protein_value(): Fetch gene protein expression value from CCLE dataset

• get_ccle_mutation_status(): Fetch gene mutation info from CCLE dataset

• get_pancan_value(): Fetch identifier value from pan-cancer dataset

• get_pancan_gene_value(): Fetch gene expression value from pan-cancer dataset

• get_pancan_transcript_value(): Fetch gene transcript expression value from pan-cancer dataset

• get_pancan_protein_value(): Fetch protein expression value from pan-cancer dataset

• get_pancan_mutation_status(): Fetch mutation status value from pan-cancer dataset

• get_pancan_cn_value(): Fetch gene copy number value from pan-cancer dataset processed by GISTIC 2.0

• get_pancan_methylation_value(): Fetch gene expression value from CCLE dataset

• get_pancan_miRNA_value(): Fetch miRNA expression value from pan-cancer dataset

• get_pcawg_gene_value(): Fetch specimen-level gene expression value from PCAWG cohort

• get_pcawg_fusion_value(): Fetch specimen-level gene fusion value from PCAWG cohort

• get_pcawg_promoter_value(): Fetch specimen-level gene promoter activity value from PCAWG cohort

• get_pcawg_miRNA_value(): Fetch specimen-level miRNA value from PCAWG cohort

• get_pcawg_APOBEC_mutagenesis_value(): Fetch specimen-level gene fusion value from PCAWG cohort

Examples

if (FALSE) {
# Fetch TP53 expression value from pan-cancer dataset
t1 <- get_pancan_value("TP53",
  dataset = "TcgaTargetGtex_rsem_isoform_tpm",
  host = "toilHub"
)
t2 <- get_pancan_gene_value("TP53")
t3 <- get_pancan_protein_value("AKT")
t4 <- get_pancan_mutation_status("TP53")
t5 <- get_pancan_cn_value("TP53")
}