get_pancan_value: Fetch Identifier Value from Pan-cancer Dataset

Description Usage Arguments Value Functions Examples

View source: R/get_pancan_value.R

Description

Identifier includes gene/probe etc.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
get_ccle_cn_value(identifier)

get_ccle_gene_value(identifier)

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)

get_pancan_transcript_value(identifier)

get_pancan_protein_value(identifier)

get_pancan_mutation_status(identifier)

get_pancan_cn_value(identifier, use_thresholded_data = TRUE)

get_pancan_methylation_value(identifier, type = c("450K", "27K"))

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_method = 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.

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.

use_thresholded_data

if TRUE (default), 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".

norm_method

the normalization method.

Value

a named vector or list.

Functions

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
## Not run: 
# 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")

## End(Not run)

UCSCXenaShiny documentation built on Nov. 29, 2021, 9:06 a.m.