In glin/brgedata: Exposures, Gene Expression and Methylation data for ilustration purpouses

Getting started

brgedata includes a collection of BRGE omic and exposome data from the same cohort. The diferent objects guarantees a minimum of samples in common between all sets.

Data available in this R package:

| Data Type | Number of Samples | Number of Features | Technology | Object Name | Class | | :------------ | ----------------: | -----------------: | :------------------------------ | :----------- | :---------------- | | Exposome | 110 | 15 | | brge_expo | ExposomeSet | | Transcriptome | 75 | 67528 | Affymetrix HTA 2.0 | brge_gexp | ExpressionSet | | Methylome | 20 | 392277 | Illumina Human Methylation 450K | brge_methy | GenomicRatioSet | | Proteome | 90 | 47 | | brge_prot | ExpressionSet |

sex and age was included as phenotipic data in each set. Moreover, the ExposomeSet includes asthma status and rhinitis status of each sample.

Data Resources

Exposome Data

To load the exposome data, stored in an ExposomeSet, run the follow commands:

data("brge_expo", package = "brgedata")
brge_expo

The summary of the data contained by brge_expo:

| Data Type | Number of Samples | Number of Features | Technology | Object Name | Class | | :------------ | ----------------: | -----------------: | :------------------------------ | :----------- | :---------------- | | Exposome | 110 | 15 | | brge_expo | ExposomeSet |

Transcriptome Data

To load the transcriptome data, saved in an ExpressionSet, run the follow commands:

data("brge_gexp", package = "brgedata")
brge_gexp

The summary of the data contained by brge_gexp:

| Data Type | Number of Samples | Number of Features | Technology | Object Name | Class | | :------------ | ----------------: | -----------------: | :------------------------------ | :----------- | :---------------- | | Transcriptome | 75 | 67528 | Affymetrix HTA 2.0 | brge_gexp | ExpressionSet |

Methylome Data

To load the methylation data, encapsulated in a GenomicRatioSet, run the follow commands:

data("brge_methy", package = "brgedata")
brge_methy

The summary of the data contained by brge_methy:

| Data Type | Number of Samples | Number of Features | Technology | Object Name | Class | | :------------ | ----------------: | -----------------: | :------------------------------ | :----------- | :---------------- | | Methylome | 20 | 392277 | Illumina Human Methylation 450K | brge_methy | GenomicRatioSet |

Proteome Data

To load the protein data, stored in an ExpressionSet, run the follow commands:

data("brge_prot", package = "brgedata")
brge_prot

The summary of the data contained by brge_prot:

| Data Type | Number of Samples | Number of Features | Technology | Object Name | Class | | :------------ | ----------------: | -----------------: | :------------------------------ | :----------- | :---------------- | | Proteome | 90 | 47 | | brge_prot | ExpressionSet |

Session info {.unnumbered}

sessionInfo()

glin/brgedata documentation built on Jan. 1, 2021, 2:22 a.m.