impcResultsCopy-methods: Retrieve a copy of IMPC results associated with a flowRepData...
In FlowRepositoryR: FlowRepository R Interface

Description Usage Arguments Details Value Author(s) Examples

This method retrieves a copy of the results associated with a parameter set of an IMPC experiment related to a flowRepData object (i.e., to a FlowRepository dataset).

1	impcResultsCopy(object, ...)

`object`	Object of class `flowRepData`.
`...`	Additional options, see the details section.

This method will return an object of class list with a copy of IMPC analysis results. This is what can typically be found in object@impc.experiments[[experimentIndex]]$ impc_parameter_sets[[resultIndex]] but without the updated_at, created_at, id, gated_by, gated_by_id, and impc_experiment_id items. You can specify the following additional options:

experimentIndex: Index of the IMPC experiment that shall be used. Usually, there is no more than 1 IMPC experiment related to a flowRepData object, but this argument is available for the odd case where there would be multiple IMPC experiments related to a single FlowRepository dataset.
resultIndex: Index of which IMPC parameter set of the IMPC experiment shall be used. When new IMPC results are submitted to FlowRepository, those will create a new paramater set associated with the particular IMPC experiment (i.e., previous results will not be overwritten). This argument can be used to specify which results are supposed to be coppied.

A list representing the results of IMPC gating. This list will usually include: impc_imm_001_001, impc_imm_002_001, impc_imm_003_001, impc_imm_004_001, impc_imm_005_001, impc_imm_006_001, impc_imm_007_001, impc_imm_008_001, impc_imm_009_001, impc_imm_010_001, impc_imm_011_001, impc_imm_012_001, impc_imm_013_001, impc_imm_014_001, impc_imm_015_001, impc_imm_016_001, impc_imm_017_001, impc_imm_018_001, impc_imm_019_001, impc_imm_020_001, impc_imm_021_001, impc_imm_022_001, impc_imm_023_001, impc_imm_024_001, impc_imm_025_001, impc_imm_026_001, impc_imm_027_001, impc_imm_028_001, impc_imm_029_001, impc_imm_030_001, impc_imm_031_001, impc_imm_032_001, impc_imm_033_001, impc_imm_034_001, impc_imm_035_001, impc_imm_036_001, impc_imm_037_001, impc_imm_038_001, impc_imm_039_001, impc_imm_040_001, impc_imm_041_001, impc_imm_042_001, impc_imm_043_001, impc_imm_044_001, impc_imm_045_001, impc_imm_046_001, impc_imm_047_001, impc_imm_048_001, impc_imm_049_001, impc_imm_050_001, impc_imm_051_001, impc_imm_052_001, impc_imm_053_001, impc_imm_054_001, impc_imm_055_001, impc_imm_056_001, impc_imm_057_001, impc_imm_058_001, impc_imm_059_001, impc_imm_060_001, impc_imm_061_001, impc_imm_062_001, impc_imm_063_001, impc_imm_064_001, impc_imm_065_001, impc_imm_066_001, impc_imm_067_001, impc_imm_068_001, impc_imm_069_001, impc_imm_070_001, impc_imm_071_001, impc_imm_072_001, impc_imm_073_001, impc_imm_074_001, impc_imm_075_001, impc_imm_076_001. Those are IMPC codes defined at https://www.mousephenotype.org/impress/protocol/174/7

Josef Spidlen

    ## Get dataset from FlowRepository
    mySmallDataset <- flowRep.get("FR-FCM-ZZ3X", impc.details = TRUE)
    impcResultsCopy(mySmallDataset, experimentIndex = 1, resultIndex = 1)
    ## The result will be NULL since the "FR-FCM-ZZ3X" does not include
    ## any IMPC details. Right now, IMPC details are only in private instances
    ## of FlowRepository. This example will be updated to a better once once
    ## IMPC data is also included and public in the main public FlowRepository
    ## (flowrepository.org).