Convert a structure into a vector

The structure is supposed to be a list. Flattening is done by extracting the given fields (return.fields) and applying the additional function (return.extra). This is mainly to be used within sapply and similar.

Usage

structure2vector(d, return.fields = NULL, return.extra = NULL)

kinetics2vector(
  d,
  condition = NULL,
  return.fields = c("Synthesis", "Half-life"),
  return.extra = NULL
)

Arguments

d

the data structure

return.fields

which fields should be extracted directly (may be NULL)

return.extra

apply a function returning a flat list or vector (may be NULL)

condition

if the original grandR object had Condition set, which condition to extract (NULL otherwise)

Value

the data flattened into a vector

Functions

• kinetics2vector(): Convert the output of the FitKinetics methods into a vector

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Condition",Design$dur.4sU,Design$Replicate))
#> Warning: Duplicate gene symbols (n=1, e.g. MATR3) present, making unique!
sars <- Normalize(sars)
fit <- FitKineticsGeneLeastSquares(sars,"SRSF6")$Mock
print(fit)
#> $data
#>            Name Condition Replicate duration.4sU duration.4sU.original no4sU
#> 1  Mock.no4sU.A      Mock         A            0                 no4sU  TRUE
#> 2     Mock.1h.A      Mock         A            1                    1h FALSE
#> 3     Mock.2h.A      Mock         A            2                    2h FALSE
#> 4     Mock.2h.B      Mock         B            2                    2h FALSE
#> 5     Mock.3h.A      Mock         A            3                    3h FALSE
#> 6     Mock.4h.A      Mock         A            4                    4h FALSE
#> 7  Mock.no4sU.A      Mock         A            0                 no4sU  TRUE
#> 8     Mock.1h.A      Mock         A            1                    1h FALSE
#> 9     Mock.2h.A      Mock         A            2                    2h FALSE
#> 10    Mock.2h.B      Mock         B            2                    2h FALSE
#> 11    Mock.3h.A      Mock         A            3                    3h FALSE
#> 12    Mock.4h.A      Mock         A            4                    4h FALSE
#>        Value  use time Type
#> 1  1352.9261 TRUE    0  Old
#> 2   949.1078 TRUE    1  Old
#> 3   694.7509 TRUE    2  Old
#> 4   814.7388 TRUE    2  Old
#> 5   546.2433 TRUE    3  Old
#> 6   328.4560 TRUE    4  Old
#> 7     0.0000 TRUE    0  New
#> 8   275.2315 TRUE    1  New
#> 9   503.5086 TRUE    2  New
#> 10  626.5115 TRUE    2  New
#> 11  672.5057 TRUE    3  New
#> 12  836.2817 TRUE    4  New
#> 
#> $residuals
#>            Name Type   Absolute    Relative
#> 1  Mock.no4sU.A  old  70.210176  0.05473556
#> 2     Mock.1h.A  old -21.017981 -0.02166521
#> 3     Mock.2h.A  old -38.961101 -0.05310136
#> 4     Mock.2h.B  old  81.026835  0.11043412
#> 5     Mock.3h.A  old  -8.667473 -0.01561958
#> 6     Mock.4h.A  old -91.226323 -0.21736992
#> 7  Mock.no4sU.A  new   0.000000         NaN
#> 8     Mock.1h.A  new -37.358670 -0.11951327
#> 9     Mock.2h.A  new -45.495290 -0.08286879
#> 10    Mock.2h.B  new  77.507573  0.14117854
#> 11    Mock.3h.A  new -55.299413 -0.07598107
#> 12    Mock.4h.A  new -26.751828 -0.03099744
#> 
#> $Synthesis
#> [1] 358.2743
#> 
#> $Degradation
#> [1] 0.2793092
#> 
#> $`Half-life`
#> [1] 2.481648
#> 
#> $conf.lower
#>   Synthesis Degradation   Half-life 
#> 316.9675391   0.2509529   2.2529248 
#> 
#> $conf.upper
#>   Synthesis Degradation   Half-life 
#> 399.5811302   0.3076655   2.7620608 
#> 
#> $f0
#> [1] 1282.716
#> 
#> $logLik
#> 'log Lik.' -64.91331 (df=3)
#> 
#> $rmse
#> [1] 54.08212
#> 
#> $rmse.new
#> [1] 46.98688
#> 
#> $rmse.old
#> [1] 60.34886
#> 
#> $total
#> [1] 7600.262
#> 
#> $type
#> [1] "equi"
#> 
kinetics2vector(fit)
#>  Synthesis  Half-life 
#> 358.274335   2.481648