se_soybean_ir_sub {bigPint} | R Documentation

## Raw and subsetted soybean leaves iron-metabolism SummarizedExperiment

### Description

This dataset contains raw RNA-sequencing read counts from a soybean dataset that compared leaves that were exposed to iron-rich (iron -postive) soil conditions versus leaves that were exposed to iron-poor (iron-negative) soil conditions. The data was collected 120 minutes after iron conditions were initiated. To save on size, this example dataset was generated by obtaining a random subset of 1 out of 10 genes from the original resource.

### Usage

    data(se_soybean_ir_sub)

### Format

(1) A DelayedMatrix with 5,604 rows and 7 variables and 1 row per gene. Accessible by `assay(se_soybean_ir_sub)`. (2) A List with 1 list element per treatment group combination and 1 row per gene. Accessible by `rowData(se_soybean_ir_sub)`.

A data frame with 5,604 rows and 7 variables

### Details

Raw and subsetted soybean leaves data SummarizedExperiment object

- `assay(se_soybean_ir_sub)` Structure:

- N.1 iron-negative condition replicate 1 raw read counts

- N.2 iron-negative condition replicate 2 raw read counts

- N.3 iron-negative condition replicate 3 raw read counts

- P.1 iron-positive condition replicate 1 raw read counts

- P.2 iron-positive condition replicate 2 raw read counts

- P.3 iron-positive condition replicate 3 raw read counts

- `rowData(se_soybean_ir_sub)` list element Structure:

- ID gene name

- logFC log fold change

- logCPM log counts per million

- LR likelihood ratio

- PValue p-value

- FDR FDR value

### References

Moran Lauter AN, Graham MA. NCBI SRA bioproject accession: PRJNA318409.

### See Also

`soybean_ir_sub` and `soybean_ir_sub_metrics`

[Package bigPint version 1.8.0 Index]