importPublicData: importPublicData

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

importPublicData

Description

Imports CAGE data from different sources into a CAGEexp object. After the object has been created the data can be further manipulated and visualized using other functions available in the CAGEr package and integrated with other analyses in R. Available resources include:

Usage

importPublicData(
  origin = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"),
  dataset,
  group,
  sample
)

## S4 method for signature 'character,character,ANY,character'
importPublicData(
  origin = c("FANTOM5", "FANTOM3and4", "ENCODE", "ZebrafishDevelopment"),
  dataset,
  group,
  sample
)

Arguments

origin	Character vector specifying one of the available resources for CAGE data ("FANTOM5", "FANTOM3and4", "ENCODE" or "ZebrafishDevelopment").
dataset	Character vector specifying one or more of the datasets available in the selected resource. For FANTOM5 it can be either "human" or "mouse", and only one of them can be specified at a time. For other resources please refer to the vignette of the corresponding data package for the list of available datasets. Multiple datasets mapped to the same genome can be specified to combine selected samples from each.
group	Character string specifying one or more groups within specified dataset(s), from which the samples should be selected. The group argument is used only when importing TSSs from data packages and ignored for "FANTOM5". For available groups in each dataset please refer to the vignette of the corresponding data package. Either only one group has to be specified (if all selected samples belong to the same group) or one group per sample (if samples belong to different groups). In the latter case, the number of elements in group must match the number of elements in sample.
sample	Character string specifying one or more CAGE samples. Check the corresponding data package for available samples within each group and their labels. For FANTOM5 resource, list of all human (~1000) and mouse (~) samples can be obtained in CAGEr by loading data(FANTOM5humanSamples) and data(FANTOM5mouseSamples), respectively. Use the names from the sample column to specify which samples should be imported.

Details

• FANTOM5 datasets (Forrest et al., Nature 2014) for numerous human and mouse samples (primary cells, cell lines and tissues), which are fetched directly from FANTOM5 online resource at https://fantom.gsc.riken.jp/5/data.

• FANTOM3 and 4 datasets (Carninci _et al., _ Science 2005, Faulkner et al., Nature Genetics 2009, Suzuki et al. Nature Genetics 2009) from FANTOM3and4CAGE data package available from Bioconductor.

• ENCODE datasets (Djebali et al. Nature 2012) for numerous human cell lines from ENCODEprojectCAGE data package, which is available for download from http://promshift.genereg.net/CAGEr/.

• Zebrafish (Danio rerio) developmental timecourse datasets (Nepal et al. Genome Research 2013) from ZebrafishDevelopmentalCAGE data package, which is available for download from http://promshift.genereg.net/CAGEr/.

Value

A CAGEexp object is returned, containing information on library size, CTSS coordinates and tag count matrix. The object is ready for CAGEr analysis (normalisation, tag clustering, …).

Author(s)

Vanja Haberle

Charles Plessy

References

• Carninci et al., (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309(5740):1559-1563.

• Djebali et al., (2012). Landscape of transcription in human cells. Nature 488(7414):101-108.

• Faulkner et al., (2009). The regulated retrotransposon transcriptome of mammalian cells., Nature Genetics 41:563-571.

• Forrest et al., (2014). A promoter-level mammalian expression atlas. Nature 507(7493):462-470.

• Nepal et al., (2013). Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research 23(11):1938-1950.

• Suzuki_et al.,_ (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line_. Nature Genetics 41:553-562.

See Also

Other FANTOM data: FANTOM5humanSamples, FANTOM5mouseSamples

Examples

## Not run: 
### importing FANTOM5 data

# list of FANTOM5 human tissue samples

data(FANTOM5humanSamples)
head(subset(FANTOM5humanSamples, type == "tissue"))

# import selected samples
f5 <- importPublicData(
  origin="FANTOM5", dataset = "human",
  sample = c("adipose_tissue__adult__pool1", "adrenal_gland__adult__pool1",
             "aorta__adult__pool1"))

CTSScoordinatesGR(f5)

### importing FANTOM3/4 data from a data package

library(FANTOM3and4CAGE)

# list of mouse datasets available in this package

data(FANTOMmouseSamples)
unique(FANTOMmouseSamples$dataset)
head(subset(FANTOMmouseSamples, dataset == "FANTOMtissueCAGEmouse"))
head(subset(FANTOMmouseSamples, dataset == "FANTOMtimecourseCAGEmouse"))

# import selected samples from two different mouse datasets

f34 <- importPublicData(
  origin="FANTOM3and4", dataset = c("FANTOMtissueCAGEmouse", "FANTOMtimecourseCAGEmouse"),
  group = c("brain", "adipogenic_induction"),
  sample = c("CCL-131_Neuro-2a_treatment_for_6hr_with_MPP+", "DFAT-D1_preadipocytes_2days"))

f34 <- importPublicData(
  origin="FANTOM3and4", dataset = c("FANTOMtissueCAGEmouse"),
  group = c("brain"),
  sample = c("CCL-131_Neuro-2a_treatment_for_6hr_with_MPP+"))

CTSScoordinatesGR(f34)


## End(Not run)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.