Convert SummarizedExperiment to contain defined treatment pair

Source: R/convertSEPair.R

Reduce a SummarizedExperiment object that initially contains more than two treatment groups to now only contain a user-specified subset pair of treatment groups. Note that this function is only necesary for users using the SummarizedExperiment input object (instead of the combination of data and dataMetrics input objects.)

convertSEPair(dataSE, group1, group2)

Arguments

dataSE

SUMMARIZEDEXPERIMENT | Summarized experiment format that can be used in lieu of data and dataMetrics
group1

CHARACTER STRING | Name of one treatment group that will remain in the dataSE object
group2

CHARACTER STRING | Name of second treatment group that will remain in the dataSE object

Value

A new dataSE object that is a subset of the input dataSE in that it now only contains the user-specified pair of treatment groups.

Examples

# Example: Read in example SummarizedExperiment object that contains three
# treatment groups (S1, S2, and S3). Reduce it to now only contain two
# treatment groups (S1 and S3).

data(se_soybean_cn_sub)
se_soybean_cn_sub_2 <- convertSEPair(se_soybean_cn_sub, "S1", "S3")