se_soybean_cn_sub {bigPint} | R Documentation

## Normalized and subsetted soybean cotyledon SummarizedExperiment

### Description

This dataset contains normalized RNA-sequencing read counts from soybean cotyledon across three time stages of development. Early stage cotyledons were collected four days after planting and were green but closed. Middle stage cotyledons were collected while green and open, soon after the plant generated its first set of unifoliate leaves. Late stage cotyledons were collected immediately after the initiation of yellowing and shrinking. 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_cn_sub)

### Format

(1) A DelayedMatrix with 7,332 rows and 10 variables and 1 row per gene. Accessible by `assay(se_soybean_cn_sub)`. (2) A List with 1 list element per treatment group combination and 1 row per gene. Accessible by `rowData(se_soybean_cn_sub)`.

### Details

Normalized and subsetted soybean cotyledon SummarizedExperiment object

- `assay(se_soybean_cn_sub)` Structure:

- S1.1 early stage replicate 1 normalized read counts

- S1.2 early stage replicate 2 normalized read counts

- S1.3 early stage replicate 3 normalized read counts

- S2.1 middle stage replicate 1 normalized read counts

- S2.2 middle stage replicate 2 normalized read counts

- S2.3 middle stage replicate 3 normalized read counts

- S3.1 late stage replicate 1 normalized read counts

- S3.2 late stage replicate 2 normalized read counts

- S3.3 late stage replicate 3 normalized read counts

- `rowData(se_soybean_cn_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

Brown AV, Hudson KA (2015) Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons. BMC Plant Biol 15:169

### See Also

`soybean_cn_sub` and `soybean_cn_sub_metrics`

[Package bigPint version 1.8.0 Index]