get_tissue_list: Retrieve Genotype-Tissue Expression (GTEx) or Human Protein...

In lagelab/Genoppi: genoppi

Retrieve Genotype-Tissue Expression (GTEx) or Human Protein Atlas specific expression data

Description

Create gene list data.frame from input traits that can be superimposed onto volcano plots or used for statistical enrichment analysis.

Usage

get_tissue_list(tissue, table = gtex_rna)

Arguments

tissue	vector of tissue names (character). See details for acceptable names.
table	datasets from genoppi: hpa_rna, hpa_protein or gtex_rna.

Details

There are three datasets available: gtex_rna, hpa_rna and hpa_protein. See ?hpa_rna, ?gtex_rna or ?gtex_protein for more details.

The following 33 tissues are available for hpa_rna:

• 'adipose tissue'

• 'adrenal gland'

• 'bone marrow'

• 'breast'

• 'cervix, uterine'

• 'ductus deferens'

• 'endometrium 1'

• 'epididymis'

• 'esophagus'

• 'fallopian tube'

• 'gallbladder'

• 'heart muscle'

• 'kidney'

• 'liver'

• 'lung'

• 'ovary'

• 'pancreas'

• 'parathyroid gland'

• 'pituitary gland'

• 'placenta'

• 'prostate'

• 'retina'

• 'salivary gland'

• 'seminal vesicle'

• 'skeletal muscle'

• 'skin 1'

• 'smooth muscle'

• 'stomach 1'

• 'testis'

• 'thyroid gland'

• 'tongue'

• 'urinary bladder'

• 'vagina'

The following 53 tissue are available for gtex_rna

• 'Adipose_Subcutaneous'

• 'Adipose_Visceral_.Omentum.'

• 'Adrenal_Gland'

• 'Artery_Aorta'

• 'Artery_Coronary'

• 'Artery_Tibial'

• 'Bladder'

• 'Brain_Amygdala'

• 'Brain_Anterior_cingulate_cortex_.BA24.'

• 'Brain_Caudate_.basal_ganglia.'

• 'Brain_Cerebellar_Hemisphere'

• 'Brain_Cerebellum'

• 'Brain_Cortex'

• 'Brain_Frontal_Cortex_.BA9.'

• 'Brain_Hippocampus'

• 'Brain_Hypothalamus'

• 'Brain_Nucleus_accumbens_.basal_ganglia.'

• 'Brain_Putamen_.basal_ganglia.'

• 'Brain_Spinal_cord_.cervical_c.1.'

• 'Brain_Substantia_nigra'

• 'Breast_Mammary_Tissue'

• 'Cells_EBV.transformed_lymphocytes'

• 'Cells_Transformed_fibroblasts'

• 'Cervix_Ectocervix'

• 'Cervix_Endocervix'

• 'Colon_Sigmoid'

• 'Colon_Transverse'

• 'Esophagus_Gastroesophageal_Junction'

• 'Esophagus_Mucosa'

• 'Esophagus_Muscularis'

• 'Fallopian_Tube'

• 'Heart_Atrial_Appendage'

• 'Heart_Left_Ventricle'

• 'Kidney_Cortex'

• 'Liver'

• 'Lung'

• 'Minor_Salivary_Gland'

• 'Muscle_Skeletal'

• 'Nerve_Tibial'

• 'Ovary'

• 'Pancreas'

• 'Pituitary'

• 'Prostate'

• 'Skin_Not_Sun_Exposed_.Suprapubic.'

• 'Skin_Sun_Exposed_.Lower_leg.'

• 'Small_Intestine_Terminal_Ileum'

• 'Spleen'

• 'Stomach'

• 'Testis'

• 'Thyroid'

• 'Uterus'

• 'Vagina'

• 'Whole_Blood'

The following 32 tissues are avialable for hpa_protein:

• 'Adrenal Gland'

• 'Artery Aorta'

• 'Artery Coronary'

• 'Artery Tibial'

• 'Brain Cerebellum'

• 'Brain Cortex'

• 'Breast'

• 'Colon Sigmoid'

• 'Colon Transverse'

• 'GE junction'

• 'Esophagus Mucosa'

• 'Esophagus Muscle'

• 'Heart Atrial'

• 'Heart Ventricle'

• 'Liver'

• 'Lung'

• 'Minor Salivary'

• 'Muscle Skeletal'

• 'Nerve Tibial'

• 'Ovary'

• 'Pancreas'

• 'Pituitary'

• 'Prostate'

• 'Skin Unexpo'

• 'Skin SunExpo'

• 'Small Intestine'

• 'Spleen'

• 'Stomach'

• 'Testis'

• 'Thyroid'

• 'Uterus'

• 'Vagina'

Examples

## Not run: 
example_data %>% 
  calc_mod_ttest() %>% 
  id_significant_proteins() %>% 
  plot_volcano_basic() %>% 
  plot_overlay(as.bait('BCL2')) %>%
  plot_overlay(list(brain = get_tissue_list("Brain_Cortex",table = gtex_rna))) %>%
  theme_volcano()

## End(Not run)

lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.