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simplify README
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@nicolerg
nicolerg authored Sep 20, 2022
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Expand Up @@ -116,224 +116,24 @@ If you can't get `devtools::install_github("MoTrPAC/MotrpacRatTraining6moData")`
```

## Explore available data objects
List available data objects after loading the package:
Find the index of available objects [here](https://motrpac.github.io/MotrpacRatTraining6moData/reference/index.html).
Click on the name of an object in this index to see its documentation.

Alternatively, explore data objects in R:
```r
# load the package
library(MotrpacRatTraining6moData)

# list available objects
data(package = "MotrpacRatTraining6moData")
```
Get the documentation for a given data object:
```r

# get the documentation for a given data object
?TRNSCRPT_LIVER_DA
```
Load a data object into your environment using `data()`:
```r
data(TRNSCRPT_LIVER_DA)
```

List of current objects:
```
ACETYL_HEART_DA Differential analysis of proteomics datasets
ACETYL_HEART_NORM_DATA Normalized protein acetylation data
ACETYL_LIVER_DA Differential analysis of proteomics datasets
ACETYL_LIVER_NORM_DATA Normalized protein acetylation data
ACETYL_META Proteomics sample-level metadata
ASSAY_ABBREV Assay or "ome" abbreviations
ASSAY_ABBREV_TO_CODE Assay abbreviation-to-code mapping
ASSAY_CODE_TO_ABBREV Assay code-to-abbreviation mapping
ASSAY_COLORS Assay colors
ASSAY_ORDER Assay order
ATAC_BAT_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_HEART_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_HIPPOC_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_KIDNEY_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_LIVER_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_LUNG_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_META ATAC-seq metadata and QC
ATAC_SKMGN_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
ATAC_WATSC_NORM_DATA_05FDR Normalized ATAC-seq data for training-regulated features
FEATURE_TO_GENE Feature-to-gene map
GENE_UNIVERSES Gene-centric universes
GRAPH_COMPONENTS Graph components
GRAPH_PW_ENRICH Graph pathway enrichment results
GRAPH_STATES 'repfdr' state assignments
GROUP_COLORS Intervention group colors
IMMUNO_ADRNL_DA Differential analysis of multiplexed immunoassays
IMMUNO_BAT_DA Differential analysis of multiplexed immunoassays
IMMUNO_COLON_DA Differential analysis of multiplexed immunoassays
IMMUNO_CORTEX_DA Differential analysis of multiplexed immunoassays
IMMUNO_HEART_DA Differential analysis of multiplexed immunoassays
IMMUNO_HIPPOC_DA Differential analysis of multiplexed immunoassays
IMMUNO_KIDNEY_DA Differential analysis of multiplexed immunoassays
IMMUNO_LIVER_DA Differential analysis of multiplexed immunoassays
IMMUNO_LUNG_DA Differential analysis of multiplexed immunoassays
IMMUNO_META Multiplexed immunoassay metadata and QC
IMMUNO_NORM_DATA_FLAT Combined immunoassay data used for visualization
IMMUNO_NORM_DATA_NESTED Processed immunoassay data used for differential analysis
IMMUNO_OVARY_DA Differential analysis of multiplexed immunoassays
IMMUNO_PLASMA_DA Differential analysis of multiplexed immunoassays
IMMUNO_SKMGN_DA Differential analysis of multiplexed immunoassays
IMMUNO_SKMVL_DA Differential analysis of multiplexed immunoassays
IMMUNO_SMLINT_DA Differential analysis of multiplexed immunoassays
IMMUNO_SPLEEN_DA Differential analysis of multiplexed immunoassays
IMMUNO_TESTES_DA Differential analysis of multiplexed immunoassays
IMMUNO_WATSC_DA Differential analysis of multiplexed immunoassays
METAB_ADRNL_DA Differential analysis of merged metabolomics datasets
METAB_ADRNL_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_BAT_DA Differential analysis of merged metabolomics datasets
METAB_BAT_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_COLON_DA Differential analysis of merged metabolomics datasets
METAB_COLON_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_CORTEX_DA Differential analysis of merged metabolomics datasets
METAB_CORTEX_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_FEATURE_ID_MAP Metabolite feature ID map
METAB_HEART_DA Differential analysis of merged metabolomics datasets
METAB_HEART_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_HIPPOC_DA Differential analysis of merged metabolomics datasets
METAB_HIPPOC_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_HYPOTH_DA Differential analysis of merged metabolomics datasets
METAB_HYPOTH_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_KIDNEY_DA Differential analysis of merged metabolomics datasets
METAB_KIDNEY_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_LIVER_DA Differential analysis of merged metabolomics datasets
METAB_LIVER_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_LUNG_DA Differential analysis of merged metabolomics datasets
METAB_LUNG_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_NORM_DATA_FLAT Combined metabolomics data used for visualization
METAB_OVARY_DA Differential analysis of merged metabolomics datasets
METAB_OVARY_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_PLASMA_DA Differential analysis of merged metabolomics datasets
METAB_PLASMA_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_SAMPLE_DATA_NESTED Nested metabolomics data used for differential analysis
METAB_SKMGN_DA Differential analysis of merged metabolomics datasets
METAB_SKMGN_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_SKMVL_DA Differential analysis of merged metabolomics datasets
METAB_SKMVL_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_SMLINT_DA Differential analysis of merged metabolomics datasets
METAB_SMLINT_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_SPLEEN_DA Differential analysis of merged metabolomics datasets
METAB_SPLEEN_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_TESTES_DA Differential analysis of merged metabolomics datasets
METAB_TESTES_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_VENACV_DA Differential analysis of merged metabolomics datasets
METAB_VENACV_DA_METAREG Meta-regression of metabolomics differential analysis results
METAB_WATSC_DA Differential analysis of merged metabolomics datasets
METAB_WATSC_DA_METAREG Meta-regression of metabolomics differential analysis results
METHYL_BAT_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_HEART_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_HIPPOC_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_KIDNEY_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_LIVER_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_LUNG_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_META RRBS metadata and QC
METHYL_SKMGN_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
METHYL_WATSC_NORM_DATA_05FDR Normalized DNA methylation data for training-regulated features
OUTLIERS Sample outliers
PATHWAY_PARENTS KEGG and Reactome parent pathways
PHENO Phenotypic data
PHOSPHO_CORTEX_DA Differential analysis of proteomics datasets
PHOSPHO_CORTEX_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_HEART_DA Differential analysis of proteomics datasets
PHOSPHO_HEART_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_KIDNEY_DA Differential analysis of proteomics datasets
PHOSPHO_KIDNEY_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_LIVER_DA Differential analysis of proteomics datasets
PHOSPHO_LIVER_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_LUNG_DA Differential analysis of proteomics datasets
PHOSPHO_LUNG_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_META Proteomics sample-level metadata
PHOSPHO_SKMGN_DA Differential analysis of proteomics datasets
PHOSPHO_SKMGN_NORM_DATA Normalized protein phosphorylation data
PHOSPHO_WATSC_DA Differential analysis of proteomics datasets
PHOSPHO_WATSC_NORM_DATA Normalized protein phosphorylation data
PROT_CORTEX_DA Differential analysis of proteomics datasets
PROT_CORTEX_NORM_DATA Normalized protein expression data
PROT_HEART_DA Differential analysis of proteomics datasets
PROT_HEART_NORM_DATA Normalized protein expression data
PROT_KIDNEY_DA Differential analysis of proteomics datasets
PROT_KIDNEY_NORM_DATA Normalized protein expression data
PROT_LIVER_DA Differential analysis of proteomics datasets
PROT_LIVER_NORM_DATA Normalized protein expression data
PROT_LUNG_DA Differential analysis of proteomics datasets
PROT_LUNG_NORM_DATA Normalized protein expression data
PROT_META Proteomics sample-level metadata
PROT_SKMGN_DA Differential analysis of proteomics datasets
PROT_SKMGN_NORM_DATA Normalized protein expression data
PROT_WATSC_DA Differential analysis of proteomics datasets
PROT_WATSC_NORM_DATA Normalized protein expression data
RAT_TO_HUMAN_GENE Rat-to-human gene ortholog map
REPEATED_FEATURES Repeated feature info
REPFDR_INPUTS 'repfdr' inputs
REPFDR_RES 'repfdr' results
SEX_COLORS Sex colors
TISSUE_ABBREV Tissue abbreviations
TISSUE_ABBREV_TO_CODE Tissue abbreviation-to-code mapping
TISSUE_CODE_TO_ABBREV Tissue code-to-abbreviation mapping
TISSUE_COLORS Tissue colors
TISSUE_ORDER Tissue order
TRAINING_REGULATED_FEATURES Training-regulated features
TRNSCRPT_ADRNL_DA Differential analysis of RNA-seq datasets
TRNSCRPT_ADRNL_NORM_DATA Normalized RNA-seq data
TRNSCRPT_ADRNL_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_BAT_DA Differential analysis of RNA-seq datasets
TRNSCRPT_BAT_NORM_DATA Normalized RNA-seq data
TRNSCRPT_BAT_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_BLOOD_DA Differential analysis of RNA-seq datasets
TRNSCRPT_BLOOD_NORM_DATA Normalized RNA-seq data
TRNSCRPT_BLOOD_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_COLON_DA Differential analysis of RNA-seq datasets
TRNSCRPT_COLON_NORM_DATA Normalized RNA-seq data
TRNSCRPT_COLON_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_CORTEX_DA Differential analysis of RNA-seq datasets
TRNSCRPT_CORTEX_NORM_DATA Normalized RNA-seq data
TRNSCRPT_CORTEX_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_HEART_DA Differential analysis of RNA-seq datasets
TRNSCRPT_HEART_NORM_DATA Normalized RNA-seq data
TRNSCRPT_HEART_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_HIPPOC_DA Differential analysis of RNA-seq datasets
TRNSCRPT_HIPPOC_NORM_DATA Normalized RNA-seq data
TRNSCRPT_HIPPOC_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_HYPOTH_DA Differential analysis of RNA-seq datasets
TRNSCRPT_HYPOTH_NORM_DATA Normalized RNA-seq data
TRNSCRPT_HYPOTH_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_KIDNEY_DA Differential analysis of RNA-seq datasets
TRNSCRPT_KIDNEY_NORM_DATA Normalized RNA-seq data
TRNSCRPT_KIDNEY_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_LIVER_DA Differential analysis of RNA-seq datasets
TRNSCRPT_LIVER_NORM_DATA Normalized RNA-seq data
TRNSCRPT_LIVER_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_LUNG_DA Differential analysis of RNA-seq datasets
TRNSCRPT_LUNG_NORM_DATA Normalized RNA-seq data
TRNSCRPT_LUNG_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_META RNA-seq metadata and QC
TRNSCRPT_OVARY_DA Differential analysis of RNA-seq datasets
TRNSCRPT_OVARY_NORM_DATA Normalized RNA-seq data
TRNSCRPT_OVARY_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_SKMGN_DA Differential analysis of RNA-seq datasets
TRNSCRPT_SKMGN_NORM_DATA Normalized RNA-seq data
TRNSCRPT_SKMGN_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_SKMVL_DA Differential analysis of RNA-seq datasets
TRNSCRPT_SKMVL_NORM_DATA Normalized RNA-seq data
TRNSCRPT_SKMVL_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_SMLINT_DA Differential analysis of RNA-seq datasets
TRNSCRPT_SMLINT_NORM_DATA Normalized RNA-seq data
TRNSCRPT_SMLINT_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_SPLEEN_DA Differential analysis of RNA-seq datasets
TRNSCRPT_SPLEEN_NORM_DATA Normalized RNA-seq data
TRNSCRPT_SPLEEN_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_TESTES_DA Differential analysis of RNA-seq datasets
TRNSCRPT_TESTES_NORM_DATA Normalized RNA-seq data
TRNSCRPT_TESTES_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_VENACV_DA Differential analysis of RNA-seq datasets
TRNSCRPT_VENACV_NORM_DATA Normalized RNA-seq data
TRNSCRPT_VENACV_RAW_COUNTS RNA-seq raw counts
TRNSCRPT_WATSC_DA Differential analysis of RNA-seq datasets
TRNSCRPT_WATSC_NORM_DATA Normalized RNA-seq data
TRNSCRPT_WATSC_RAW_COUNTS RNA-seq raw counts
UBIQ_HEART_DA Differential analysis of proteomics datasets
UBIQ_HEART_NORM_DATA Normalized protein ubiquitynation data
UBIQ_LIVER_DA Differential analysis of proteomics datasets
UBIQ_LIVER_NORM_DATA Normalized protein ubiquitynation data
UBIQ_META Proteomics sample-level metadata
# load a data object into your environment using `data()`
data(TRNSCRPT_LIVER_DA)
# or just use it directly, e.g.,
head(TRNSCRPT_LIVER_DA)
```

## Access epigenomics data through Google Cloud Storage
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