FlowRepositoryR (version 1.4.0)

impcResultsCopy: Retrieve a copy of IMPC results associated with a flowRepData object

Description

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).

Usage

impcResultsCopy(object, ...)

Arguments

object

Object of class flowRepData.

...

Additional options, see the details section.

Value

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

Details

This method will return an object of class list with a copy of IMPC analysis results. This is what can typically be found in [e-mail][[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.

Examples

    ## 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).