Replace missing values with a proportion of the row minimum
Source:R/functions-imputation.R
imputeRowMin.RdimputeRowMin imputes missing values in x by replacing NAs in each row
with a proportion of the minimal value for that row (i.e.
min_fraction * min(x[i, ])).
Arguments
- x
matrixwith abundances, rows being features/metabolites and columns samples.- min_fraction
numeric(1)with the fraction of the row minimum that should be used to replaceNAvalues in that row.
See also
imputeLCMD package for more left censored imputation functions.
Other imputation functions:
imputeRowMinRand()
Examples
library(MSnbase)
library(faahKO)
data("faahko")
xset <- group(faahko)
mat <- groupval(xset, value = "into")
mat_imp <- imputeRowMin(mat)
head(mat)
#> ko15 ko16 ko18 ko19 ko21 ko22
#> 200.1/2926 147887.5 451600.7 65290.38 NA 91635.45 162012.4
#> 205/2791 1778568.9 1567038.1 1482796.38 1039129.8 1223132.35 1072037.7
#> 206/2790 237993.6 269714.0 201393.42 150107.3 176989.65 156797.0
#> 207.1/2719 380873.0 460629.7 351750.14 219288.0 286848.56 235022.6
#> 219.1/2525 235544.9 173623.4 NA NA 185792.43 174458.8
#> 231/2517 NA NA 222609.07 286232.1 435094.49 NA
#> wt15 wt16 wt18 wt19 wt21 wt22
#> 200.1/2926 175177.1 82619.48 NA 69198.22 153273.5 98144.28
#> 205/2791 1950287.5 1466780.60 1572679.16 1275312.76 1356014.3 1231442.16
#> 206/2790 276541.8 222366.15 211717.71 186850.88 188285.9 172348.76
#> 207.1/2719 417169.6 324892.46 277990.70 220972.35 252874.0 236728.16
#> 219.1/2525 244584.5 161184.05 72029.38 NA 238194.4 173829.95
#> 231/2517 NA NA NA 240261.21 201316.2 179437.72
head(mat_imp)
#> ko15 ko16 ko18 ko19 ko21 ko22
#> 200.1/2926 147887.53 451600.71 65290.38 32645.19 91635.45 162012.44
#> 205/2791 1778568.94 1567038.14 1482796.38 1039129.82 1223132.35 1072037.70
#> 206/2790 237993.62 269713.98 201393.42 150107.31 176989.65 156797.04
#> 207.1/2719 380873.05 460629.74 351750.14 219287.97 286848.56 235022.63
#> 219.1/2525 235544.92 173623.38 36014.69 36014.69 185792.43 174458.77
#> 231/2517 89718.86 89718.86 222609.07 286232.15 435094.49 89718.86
#> wt15 wt16 wt18 wt19 wt21 wt22
#> 200.1/2926 175177.08 82619.48 32645.19 69198.22 153273.5 98144.28
#> 205/2791 1950287.49 1466780.60 1572679.16 1275312.76 1356014.3 1231442.16
#> 206/2790 276541.85 222366.15 211717.71 186850.88 188285.9 172348.76
#> 207.1/2719 417169.58 324892.46 277990.70 220972.35 252874.0 236728.16
#> 219.1/2525 244584.47 161184.05 72029.38 36014.69 238194.4 173829.95
#> 231/2517 89718.86 89718.86 89718.86 240261.21 201316.2 179437.72
## Replace with 1/8 of the row mimimum
head(imputeRowMin(mat, min_fraction = 1/8))
#> ko15 ko16 ko18 ko19 ko21 ko22
#> 200.1/2926 147887.53 451600.71 65290.385 8161.298 91635.45 162012.44
#> 205/2791 1778568.94 1567038.14 1482796.385 1039129.818 1223132.35 1072037.70
#> 206/2790 237993.62 269713.98 201393.415 150107.310 176989.65 156797.04
#> 207.1/2719 380873.05 460629.74 351750.138 219287.968 286848.56 235022.63
#> 219.1/2525 235544.92 173623.38 9003.672 9003.672 185792.43 174458.77
#> 231/2517 22429.72 22429.72 222609.068 286232.146 435094.49 22429.72
#> wt15 wt16 wt18 wt19 wt21 wt22
#> 200.1/2926 175177.08 82619.48 8161.298 69198.222 153273.5 98144.28
#> 205/2791 1950287.49 1466780.60 1572679.161 1275312.758 1356014.3 1231442.16
#> 206/2790 276541.85 222366.15 211717.713 186850.878 188285.9 172348.76
#> 207.1/2719 417169.58 324892.46 277990.701 220972.352 252874.0 236728.16
#> 219.1/2525 244584.47 161184.05 72029.378 9003.672 238194.4 173829.95
#> 231/2517 22429.72 22429.72 22429.715 240261.212 201316.2 179437.72