Compare a feature variable overlap

Extracts qualitative feature variables from two MSnSet instances and compares with a contingency table.

checkFvarOverlap(x, y, fcolx = "markers", fcoly, verbose = TRUE)

Arguments

x

An MSnSet instance.

y

An MSnSet instance.

fcolx

The feature variable to separate unknown (fData(y)$coly == "unknown") from the marker features in the x object.

fcoly

As fcolx, for the y object. If missing, the value of fcolx is used.

verbose

If TRUE (default), the contingency table of the the feature variables is printed out.

Value

Invisibly returns a named list with the values of the diagonal, upper and lower triangles of the contingency table.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
res <- checkFvarOverlap(dunkley2006, dunkley2006,
                        "markers", "markers.orig")
#>                my
#> mx               ER Golgi  PM mit/plastid unknown vacuole
#>   ER lumen       11     0   0           0       3       0
#>   ER membrane    21     0   0           0      24       0
#>   Golgi           0    27   0           0       1       0
#>   Mitochondrion   0     0   0          13      42       0
#>   PM              0     0  28           0      18       0
#>   Plastid         0     0   0           7      13       0
#>   Ribosome        0     0   0           0      19       0
#>   TGN             0     0   0           0      13       0
#>   unknown        17     0   0           6     405       0
#>   vacuole         0     0   0           0       9      12
str(res)
#> List of 3
#>  $ matches         : int [1:6] 11 0 0 13 18 0
#>  $ lower.mismatches: int [1:39] 21 0 0 0 0 0 0 17 0 27 ...
#>  $ upper.mismatches: int [1:39] 21 0 0 0 0 0 0 17 0 27 ...