analysis_settings_v1.0.Rmd

```{r}
CONFIG <- list(
    # general
    'pathogen'            = 'NULL',
    'host'                = 'H. sapiens',
    'target'              = 'host',
    'analysis_name'       = 'russell_etal',

    # sample variables of interest
    'sample_id'           = 'sample',
    'condition'           = 'group',
    'batch'               = 'batch',
    
    # Covariates
    'covariates'          = c('batch', 'sex', 'age'),  # Vector of one or more sample covariates to test for correlation with expression


    # sample metadata
    'samples'             = tbl_df(read.delim("/net/isi-dcnl/ifs/user_data/kmorris/Group/omeally/CGT.shevchenko.mRNAseq.T1D_Bcells.Jan2020/devel/russell_etal/coldata.txt")),

    # input count tables
    "input_count_tables"  = file.path('/net/isi-dcnl/ifs/user_data/kmorris/Group/omeally/CGT.shevchenko.mRNAseq.T1D_Bcells.Jan2020/devel/russell_etal/merged_gene_counts_modified.txt'),

    # normalization / data transformation
    'de_cpm'                 = TRUE,
    'de_log2'                = TRUE,
    'de_voom'                = TRUE,
    'de_quantile_normalize'  = TRUE,
    'de_batch_adjust'        = 'combat',

    # annotations
    "organism_db"         = "Homo.sapiens",
    "orgdb_key"           = "ENSEMBL",
    "organism_genome"     = "hg38",
    "biomart_dataset"     = "hsapiens_gene_ensembl",

    # differential expression
    "contrast_column"  = 'group',
    "de_comparisons"   = list(c('control', 'T1D'))
)
```