rnaseq_plan: Execute the drake RNA-seq plan

Description Usage Arguments

View source: R/plan.R

Description

This function wraps the "drake::plan()".

Usage

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rnaseq_plan(
  metadata_id,
  metadata_version,
  counts_id,
  counts_version,
  gene_id_input,
  factor_input,
  continuous_input,
  gene_id,
  biomart_id,
  biomart_version,
  host,
  filters,
  organism,
  conditions
)

Arguments

metadata_id

Synapse ID to clean metadata file with sample identifiers in a column and variables of interest as column names. There cannot be any missing values.

metadata_version

Optionally, include Synapse file version number. If omitted, current version will be downloaded.

counts_id

Synapse ID to counts data frame with identifiers to the metadata as column names and gene ids in a column.

counts_version

Optionally, include Synapse file version number.

gene_id_input

Column name of the gene ids in the counts_id file.

factor_input

Vector of factor variables. Variables must be present in the metadata as column names.

continuous_input

Vector of continuous variables. Variables must be present in the metadata as column names.

gene_id

Column name of gene Ids

biomart_id

Synapse ID to biomart object.

biomart_version

Optionally, include Synapse file version number.

host

An optional character vector specifying the release version. This specification is highly recommended for a reproducible workflow. (see "biomaRt::listEnsemblArchives()")

filters

A character vector listing biomaRt query filters. (For a list of filters see "biomaRt::listFilters()")

organism

A character vector of the organism name. This argument takes partial strings. For example,"hsa" will match "hsapiens_gene_ensembl".

conditions

Conditions to bin gene counts that correspond to variables in 'md'.


jgockley62/UW_RNASeq documentation built on Oct. 1, 2020, 8:07 p.m.