get_all_ceRNAInteractions: Find All Possible ceRNA Interactions

Description Usage Arguments Value Examples

View source: R/all_ceRNAInteraction.R

Description

Get all ceRNA interactions by given identifications (ensg_number, gene_symbol or gene_type), specific cancer type/dataset or different filter possibilities according different statistical values (e.g. FDR adjusted p-value).

Usage

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get_all_ceRNAInteractions(
  disease_name = NULL,
  ensg_number = NULL,
  gene_symbol = NULL,
  gene_type = NULL,
  pValue = 0.05,
  pValueDirection = "<",
  mscor = NULL,
  mscorDirection = "<",
  correlation = NULL,
  correlationDirection = "<",
  sorting = NULL,
  descending = TRUE,
  limit = 100,
  offset = NULL,
  information = FALSE
)

Arguments

disease_name

Name of the specific cancer type/dataset. If default is set, all available datasets with corresponding informations are shown. Fuzzy search available.

ensg_number

A vector of ensg number(s). If ensg number is set, gene symbol and gene type must be NULL. One of the three identifiers must be provided.

gene_symbol

A vector of gene symbol(s). If gene symbol is set, ensg number and gene type must be NULL. One of the three identifiers must be provided.

gene_type

Defines the type of gene of interest. One out of [3prime_overlapping_ncRNA, antisense, antisense_RNA, bidirectional_promoter_lncRNA, IG_C_gene, IG_C_pseudogene, IG_V_gene, IG_V_pseudogene, lincRNA, macro_lncRNA, miRNA, misc_RNA, Mt_rRNA, polymorphic_pseudogene, processed_pseudogene, processed_transcript, protein_coding, pseudogene, ribozyme, rRNA, rRNA_pseudogene, scaRNA, scRNA, sense_intronic, sense_overlapping, snoRNA, snRNA, TEC, TR_C_gene, TR_V_gene, TR_V_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, translated_processed_pseudogene, unitary_pseudogene, unprocessed_pseudogene, vaultRNA].

pValue

Threshold of the FDR adjusted p-value. Default is 0.05.

pValueDirection

Direction of the FDR adjusted p-value threshold (<, >). Must be set if pValue is set. Possible values are: "<", ">".

mscor

Threshold of the 'multiple sensitivity correlation' (mscor).

mscorDirection

Direction of the mscor threshold (<, >). Must be set if pValue is set. Possible values are: "<", ">".

correlation

Threshold of the correlation.

correlationDirection

Direction of the correlation threshold (<, >). Must be set if pValue is set. Possible values are: "<", ">".

sorting

Possibilities for sorting of the results. Possible values are "pValue", "mscor" or "correlation".

descending

Descending (TRUE, default) or ascending (FALSE) ordering of the results.

limit

Number of results that should be shown. Default value is 100 and can be up to 1000. For more results please use batches, the provided offset parameter or download the whole dataset.

offset

Starting point from where results should be shown.

information

All available information about genes displayed (TRUE) or just ensg number (FALSE, default).

Value

A data_frame containing all ceRNA interactions fitting the paramters.

Examples

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# Retrieve all possible ceRNAs for gene, identified by ensg_number,
# and threshold for pValue and mscor.
get_all_ceRNAInteractions(ensg_number=c("ENSG00000259090","ENSG00000217289"),
                          pValue=0.5, pValueDirection="<",
                          mscor=0.006, mscorDirection="<",
                          limit=15, information=FALSE)

IceQueen1996/spongeAPI documentation built on March 8, 2021, 8:33 p.m.