Filtering sets of chromatographic data — filterColumnsIntensityAbove,MChromatograms-method • xcms

These functions allow to filter (subset) MSnbase::MChromatograms() or XChromatograms() objects, i.e. sets of chromatographic data, without changing the data (intensity and retention times) within the individual chromatograms (MSnbase::Chromatogram() objects).

filterColumnsIntensityAbove: subsets a MChromatograms objects keeping only columns (samples) for which value is larger than the provided threshold in which rows (i.e. if which = "any" a column is kept if any of the chromatograms in that column have a value larger than threshold or with which = "all" all chromatograms in that column fulfill this criteria). Parameter value allows to define on which value the comparison should be performed, with value = "bpi" the maximum intensity of each chromatogram is compared to threshold, with value = "tic" the total sum of intensities of each chromatogram is compared to threshold. For XChromatogramsobject,value = "maxo"andvalue = "into"are supported which compares the largest intensity of all identified chromatographic peaks in the chromatogram withthreshold`, or the integrated peak area, respectively.
filterColumnsKeepTop: subsets a MChromatograms object keeping the top n columns sorted by the value specified with sortBy. In detail, for each column the value defined by sortBy is extracted from each chromatogram and aggregated using the aggregationFun. Thus, by default, for each chromatogram the maximum intensity is determined (sortBy = "bpi") and these values are summed up for chromatograms in the same column (aggregationFun = sum). The columns are then sorted by these values and the top n columns are retained in the returned MChromatograms. Similar to the filterColumnsIntensityAbove function, this function allows to use for XChromatograms objects to sort the columns by column sortBy = "maxo" or sortBy = "into" of the chromPeaks matrix.

Usage

# S4 method for class 'MChromatograms'
filterColumnsIntensityAbove(
  object,
  threshold = 0,
  value = c("bpi", "tic"),
  which = c("any", "all")
)

# S4 method for class 'MChromatograms'
filterColumnsKeepTop(
  object,
  n = 1L,
  sortBy = c("bpi", "tic"),
  aggregationFun = sum
)

# S4 method for class 'XChromatograms'
filterColumnsIntensityAbove(
  object,
  threshold = 0,
  value = c("bpi", "tic", "maxo", "into"),
  which = c("any", "all")
)

# S4 method for class 'XChromatograms'
filterColumnsKeepTop(
  object,
  n = 1L,
  sortBy = c("bpi", "tic", "maxo", "into"),
  aggregationFun = sum
)

Arguments

object: MSnbase::MChromatograms() or XChromatograms() object.
threshold: for filterColumnsIntensityAbove: numeric(1) with the threshold value to compare against.
value: character(1) defining which value should be used in the comparison or sorting. Can be value = "bpi" (default) to use the maximum intensity per chromatogram or value = "tic" to use the sum of intensities per chromatogram. For XChromatograms() objects also value = "maxo" and value = "into" is supported to use the maximum intensity or the integrated area of identified chromatographic peaks in each chromatogram.
which: for filterColumnsIntensityAbove: character(1) defining whether any (which = "any", default) or all (which = "all") chromatograms in a column have to fulfill the criteria for the column to be kept.
n: for filterColumnsKeepTop: integer(1) specifying the number of columns that should be returned. n will be rounded to the closest (larger) integer value.
sortBy: for filterColumnsKeepTop: the value by which columns should be ordered to determine the top n columns. Can be either sortBy = "bpi" (the default), in which case the maximum intensity of each column's chromatograms is used, or sortBy = "tic" to use the total intensity sum of all chromatograms. For XChromatograms() objects also value = "maxo" and value = "into" is supported to use the maximum intensity or the integrated area of identified chromatographic peaks in each chromatogram.
aggregationFun: for filterColumnsKeepTop: function to be used to aggregate (combine) the values from all chromatograms in each column. Defaults to aggregationFun = sum in which case the sum of the values is used to rank the columns. Alternatively the mean, median or similar function can be used.

Value

a filtered MChromatograms (or XChromatograms) object with the same number of rows (EICs) but eventually a lower number of columns (samples).

Author

Johannes Rainer

Examples


library(MSnbase)
chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
    intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
    intensity = c(80, 50, 20, 10, 9, 4, 3, 4, 1, 3))
chr3 <- Chromatogram(rtime = 3:9 + rnorm(7, sd = 0.3),
    intensity = c(53, 80, 130, 15, 5, 3, 2))

chrs <- MChromatograms(list(chr1, chr2, chr1, chr3, chr2, chr3),
    ncol = 3, byrow = FALSE)
chrs
#> MChromatograms with 2 rows and 3 columns
#>                   1              2              3
#>      <Chromatogram> <Chromatogram> <Chromatogram>
#> [1,]     length: 10     length: 10     length: 10
#> [2,]     length: 10      length: 7      length: 7
#> phenoData with 0 variables
#> featureData with 0 variables

#### filterColumnsIntensityAbove
##
## Keep all columns with for which the maximum intensity of any of its
## chromatograms is larger 90
filterColumnsIntensityAbove(chrs, threshold = 90)
#> MChromatograms with 2 rows and 3 columns
#>                   1              2              3
#>      <Chromatogram> <Chromatogram> <Chromatogram>
#> [1,]     length: 10     length: 10     length: 10
#> [2,]     length: 10      length: 7      length: 7
#> phenoData with 0 variables
#> featureData with 0 variables

## Require that ALL chromatograms in a column have a value larger 90
filterColumnsIntensityAbove(chrs, threshold = 90, which = "all")
#> MChromatograms with 2 rows and 1 column
#>                   2
#>      <Chromatogram>
#> [1,]     length: 10
#> [2,]      length: 7
#> phenoData with 0 variables
#> featureData with 0 variables

## If none of the columns fulfills the criteria no columns are returned
filterColumnsIntensityAbove(chrs, threshold = 900)
#> MChromatograms with 2 rows and 0 columns
#> phenoData with 0 variables
#> featureData with 0 variables

## Filtering XChromatograms allow in addition to filter on the columns
## "maxo" or "into" of the identified chromatographic peaks within each
## chromatogram.

#### filterColumnsKeepTop
##
## Keep the 2 columns with the highest sum of maximal intensities in their
## chromatograms
filterColumnsKeepTop(chrs, n = 1)
#> MChromatograms with 2 rows and 1 column
#>                   2
#>      <Chromatogram>
#> [1,]     length: 10
#> [2,]      length: 7
#> phenoData with 0 variables
#> featureData with 0 variables

## Keep the 50 percent of columns with the highest total sum of signal. Note
## that n will be rounded to the next larger integer value
filterColumnsKeepTop(chrs, n = 0.5 * ncol(chrs), sortBy = "tic")
#> MChromatograms with 2 rows and 2 columns
#>                   2              3
#>      <Chromatogram> <Chromatogram>
#> [1,]     length: 10     length: 10
#> [2,]      length: 7      length: 7
#> phenoData with 0 variables
#> featureData with 0 variables