This function wraps the "drake::plan()"
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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
)
|
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 |
filters |
A character vector listing biomaRt query filters.
(For a list of filters see |
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'. |
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