assembleBiologicProject: assembleBiologicProject
In decusInLabore/biologicSeqTools2: Seq Analysis Helper Functions

assembleBiologicProject

R Documentation

assembleBiologicProject

Description

This function creates a settings file for a biologic data visualization project.

Usage

assembleBiologicProject(
  genome = NULL,
  primaryAlignmentGeneID = NULL,
  release = "release-89",
  species = NULL,
  path2GeneIDtable = NULL,
  GTFfile = NULL,
  genomeFa = NULL,
  genomeFai = NULL,
  rRNAfile = NULL,
  geneIDcolumn = NULL,
  refFlatFile = NULL,
  ribosomalIntervalList = NULL,
  genomeidx = NULL,
  bowtieGenomeidx = NULL,
  designFN = NULL,
  modelFN = NULL,
  NFcoreSettingsFN = NULL,
  countTableFN = NULL,
  TpmTableFN = NULL,
  PcaFN = NULL,
  mostVariableFeaturesFN = NULL,
  calculate_DGE = TRUE,
  calculate_LRT = TRUE,
  DEseq2External_DGE = NULL,
  DEseq2External_LRT = NULL,
  projectFolder = NULL,
  experiment_id = NULL,
  title = NULL,
  subtitle = NULL,
  abstract = NULL,
  project_name = NULL,
  lims.id = NULL,
  labname = NULL,
  NtopGenes = NULL,
  corGeneVec = NULL,
  experiment.type = NULL,
  count.table.headline = "TPM-values for all Samples",
  count.table.sidelabel = "TPM",
  heatmap.headline.text = "Heatmap: Row-averaged Expr",
  designTScol = NULL,
  timecourse.units = NULL,
  primDataDB = NULL,
  db.user = NULL,
  host = NULL,
  port = 6008,
  lab.categories.table = NULL,
  HGtestEnrichmentGmtFile = NULL,
  GSEAtestEnrichmentGmtFile = NULL,
  pathToSeqStorageFolder = NULL,
  stranded = FALSE,
  read.length = "100bp",
  paired.end = FALSE,
  pathToRSEMresultsFiles = NULL,
  dfRef = NULL,
  biologicSettingsFN = NULL
)

Arguments

`genome`	Genome ID, e.g. GRCm38
`release`	Ensembl release used for annotations. Option: "release-89",
`species`	Species. Options: "homo_sapiens", "mus_musculus", "drosophila_melongaster", "daniero_rerio"
`designFN`	Path to a design file.
`modelFN`	Path to DGE model file
`NFcoreSettingsFN`	Path to NF core settings file.
`countTableFN`	Path to count table
`TpmTableFN`	Path to TPM table
`PcaFN`	Path to PCA table
`mostVariableFeaturesFN`	Path to most variable featurs file
`calculate_DGE`	If DGE instructions are present in the desing file, calculate
`calculate_LRT`	If LRT instructions are present in the desing file, calculate
`DEseq2External_DGE`	Folder in which external res(dds) results are kept
`DEseq2External_LRT`	Folder in which external res(dds) results are kept
`projectFolder`	Path to project folder
`experiment_id`	Experiment ID
`title`	Experiment title
`subtitle`	Experiment subtitle - usually labnane - lead scientis
`abstract`	Abstract
`project_name`	Project name
`lims.id`	LIMS ID to retrieve meta data
`labname`	Labname
`NtopGenes`	Ntopgenes to use for PCA
`corGeneVec`	Vector with genes to calculate correlations for
`experiment.type`	Experiment type: options: "bulk_rna_seq", "sc_rna_seq", "mi_rna_seq"
`count.table.headline`	String to be displayed in count table headlines
`count.table.sidelabel`	String to be displayed as count table sidelabel
`heatmap.headline.text`	Heatmap headline text
`designTScol`	Column name of a numeric column in the design file
`timecourse.units`	Timecourse units
`primDataDB`	Primary database
`db.user`	Database username
`host`	Database host IP
`lab.categories.table`	Lab categories table
`HGtestEnrichmentGmtFile`	HGtestEnrichmentGmtFile vector
`GSEAtestEnrichmentGmtFile`	GSEAtestEnrichmentGmtFile vector
`pathToSeqStorageFolder`	Vector of paths to folders to Crick sequencing storage. Make sure the last character is a /
`stranded`	Boolean
`read.length`	default 100bp
`paired.end`	Boolean
`pathToRSEMresultsFiles`	pathToRSEMresultsFiles
`dfRef`	Dataframe for reference files
`excelList`	A list of dataframes
`outPutFN`	A output filepath/filename