parse_aracne: Parse inputs (from aracne-ap_viper Nextflow)
In brucemoran/RNAseqR: RNAseq DE Analysis Downstream from Nextflow Pipelines
Description
Usage
Arguments
Value
View source: R/aracne-ap_viper.R
Description
Parse inputs (from aracne-ap_viper Nextflow)
Usage
1
parse_aracne(NETWORK, EXPRMAT, METADATA, TAG, genome_prefix = "hsapiens")
Arguments
NETWORK
ARACNe_AP network file
EXPRMAT
expression matrix in tab-separated format:
header line in format:
geneID sample_1 ... sampleID_n
all other lines in format
geneID_1 value_1 ... value_n etc.
METADATA
metadata to discriminate between cohorts for msViper analysis;
tab-separated format; header line format:
sample group
all other lines:
sampleID_1 group_0 etc.
TAG
string identifier of the run
genome_prefix
string of a genome in biomart$dataset, suffixed with
'_gene_ensembl'
Value
none, saves two RData files to current dir contianing:
ensembl to external gene mapping (en2ext);
combined.eset, regulonaracne required to run msViper
brucemoran/RNAseqR documentation built on Sept. 14, 2021, 11:08 a.m.
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Description Usage Arguments Value
View source: R/aracne-ap_viper.R
Description
Parse inputs (from aracne-ap_viper Nextflow)
Usage
1 | parse_aracne(NETWORK, EXPRMAT, METADATA, TAG, genome_prefix = "hsapiens")
|
Arguments
NETWORK |
ARACNe_AP network file |
EXPRMAT |
expression matrix in tab-separated format: header line in format: geneID sample_1 ... sampleID_n all other lines in format geneID_1 value_1 ... value_n etc. |
METADATA |
metadata to discriminate between cohorts for msViper analysis; tab-separated format; header line format: sample group all other lines: sampleID_1 group_0 etc. |
TAG |
string identifier of the run |
genome_prefix |
string of a genome in biomart$dataset, suffixed with '_gene_ensembl' |
Value
none, saves two RData files to current dir contianing: ensembl to external gene mapping (en2ext); combined.eset, regulonaracne required to run msViper
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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