binYonX: Aggregate values in y for bins defined on x

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Aggregate values in y for bins defined on x

Description

This functions takes two same-sized numeric vectors x and y, bins/cuts x into bins (either a pre-defined number of equal-sized bins or bins of a pre-defined size) and aggregates values in y corresponding to x values falling within each bin. By default (i.e. method = "max") the maximal y value for the corresponding x values is identified. x is expected to be incrementally sorted and, if not, it will be internally sorted (in which case also y will be ordered according to the order of x).

Usage

binYonX(x, y, breaks, nBins, binSize, binFromX, binToX, fromIdx = 1L,
  toIdx = length(x), method = "max", baseValue,
  sortedX = !is.unsorted(x), shiftByHalfBinSize = FALSE,
  returnIndex = FALSE, returnX = TRUE)

Arguments

x	Numeric vector to be used for binning.
y	Numeric vector (same length than x) from which the maximum values for each bin should be defined. If not provided, x will be used.
breaks	Numeric vector defining the breaks for the bins, i.e. the lower and upper values for each bin. See examples below.
nBins	integer(1) defining the number of desired bins.
binSize	numeric(1) defining the desired bin size.
binFromX	Optional numeric(1) allowing to manually specify the range of x-values to be used for binning. This will affect only the calculation of the breaks for the bins (i.e. if nBins or binSize is provided). If not provided the minimal value in the sub-set fromIdx-toIdx in input vector x will be used.
binToX	Same as binFromX, but defining the maximum x-value to be used for binning.
fromIdx	Integer vector defining the start position of one or multiple sub-sets of input vector x that should be used for binning.
toIdx	Same as toIdx, but defining the maximum index (or indices) in x to be used for binning.
method	A character string specifying the method that should be used to aggregate values in y. Allowed are "max", "min", "sum" and "mean" to identify the maximal or minimal value or to sum all values within a bin or calculate their mean value.
baseValue	The base value for empty bins (i.e. bins into which either no values in x did fall, or to which only NA values in y were assigned). By default (i.e. if not specified), NA is assigned to such bins.
sortedX	Whether x is sorted.
shiftByHalfBinSize	Logical specifying whether the bins should be shifted by half the bin size to the left. Thus, the first bin will have its center at fromX and its lower and upper boundary are fromX - binSize/2 and fromX + binSize/2. This argument is ignored if breaks are provided.
returnIndex	Logical indicating whether the index of the max (if method = "max") or min (if method = "min") value within each bin in input vector x should also be reported. For methods other than "max" or "min" this argument is ignored.
returnX	logical allowing to avoid returning $x, i.e. the mid-points of the bins. returnX = FALSE might be useful in cases where breaks are pre-defined as it considerably reduces the memory demand.

Details

The breaks defining the boundary of each bin can be either passed directly to the function with the argument breaks, or are calculated on the data based on arguments nBins or binSize along with fromIdx, toIdx and optionally binFromX and binToX. Arguments fromIdx and toIdx allow to specify subset(s) of the input vector x on which bins should be calculated. The default the full x vector is considered. Also, if not specified otherwise with arguments binFromX and binToX , the range of the bins within each of the sub-sets will be from x[fromIdx] to x[toIdx]. Arguments binFromX and binToX allow to overwrite this by manually defining the a range on which the breaks should be calculated. See examples below for more details.

Calculation of breaks: for nBins the breaks correspond to seq(min(x[fromIdx])), max(x[fromIdx], length.out = (nBins + 1)). For binSize the breaks correspond to seq(min(x[fromIdx]), max(x[toIdx]), by = binSize) with the exception that the last break value is forced to be equal to max(x[toIdx]). This ensures that all values from the specified range are covered by the breaks defining the bins. The last bin could however in some instances be slightly larger than binSize. See breaks_on_binSize and breaks_on_nBins for more details.

Value

Returns a list of length 2, the first element (named "x") contains the bin mid-points, the second element (named "y") the aggregated values from input vector y within each bin. For returnIndex = TRUE the list contains an additional element "index" with the index of the max or min (depending on whether method = "max" or method = "min") value within each bin in input vector x.

Note

The function ensures that all values within the range used to define the breaks are considered in the binning (and assigned to a bin). This means that for all bins except the last one values in x have to be >= xlower and < xupper (with xlower and xupper being the lower and upper boundary, respectively). For the last bin the condition is x >= xlower & x <= xupper. Note also that if shiftByHalfBinSize is TRUE the range of values that is used for binning is expanded by binSize (i.e. the lower boundary will be fromX - binSize/2, the upper toX + binSize/2). Setting this argument to TRUE resembles the binning that is/was used in profBin function from xcms < 1.51.

NA handling: by default the function ignores NA values in y (thus inherently assumes na.rm = TRUE). No NA values are allowed in x.

Author(s)

Johannes Rainer

See Also

imputeLinInterpol

Examples

########
## Simple example illustrating the breaks and the binning.
##
## Define breaks for 5 bins:
brks <- seq(2, 12, length.out = 6)
## The first bin is then [2,4), the second [4,6) and so on.
brks
## Get the max value falling within each bin.
binYonX(x = 1:16, y = 1:16, breaks = brks)
## Thus, the largest value in x = 1:16 falling into the bin [2,4) (i.e. being
## >= 2 and < 4) is 3, the largest one falling into [4,6) is 5 and so on.
## Note however the function ensures that the minimal and maximal x-value
## (in this example 1 and 12) fall within a bin, i.e. 12 is considered for
## the last bin.

#######
## Performing the binning ons sub-set of x
##
X <- 1:16
## Bin X from element 4 to 10 into 5 bins.
X[4:10]
binYonX(X, X, nBins = 5L, fromIdx = 4, toIdx = 10)
## This defines breaks for 5 bins on the values from 4 to 10 and bins
## the values into these 5 bins. Alternatively, we could manually specify
## the range for the binning, i.e. the minimal and maximal value for the
## breaks:
binYonX(X, X, nBins = 5L, fromIdx = 4, toIdx = 10, binFromX = 1, binToX = 16)
## In this case the breaks for 5 bins were defined from a value 1 to 16 and
## the values 4 to 10 were binned based on these breaks.

#######
## Bin values within a sub-set of x, second example
##
## This example illustrates how the fromIdx and toIdx parameters can be used.
## x defines 3 times the sequence form 1 to 10, while y is the sequence from
## 1 to 30. In this very simple example x is supposed to represent M/Z values
## from 3 consecutive scans and y the intensities measured for each M/Z in
## each scan. We want to get the maximum intensities for M/Z value bins only
## for the second scan, and thus we use fromIdx = 11 and toIdx = 20. The breaks
## for the bins are defined with the nBins, binFromX and binToX.
X <- rep(1:10, 3)
Y <- 1:30
## Bin the M/Z values in the second scan into 5 bins and get the maximum
## intensity for each bin. Note that we have to specify sortedX = TRUE as
## the x and y vectors would be sorted otherwise.
binYonX(X, Y, nBins = 5L, sortedX = TRUE, fromIdx = 11, toIdx = 20)

#######
## Bin in overlapping sub-sets of X
##
## In this example we define overlapping sub-sets of X and perform the binning
## within these.
X <- 1:30
## Define the start and end indices of the sub-sets.
fIdx <- c(2, 8, 21)
tIdx <- c(10, 25, 30)
binYonX(X, nBins = 5L, fromIdx = fIdx, toIdx = tIdx)
## The same, but pre-defining also the desired range of the bins.
binYonX(X, nBins = 5L, fromIdx = fIdx, toIdx = tIdx, binFromX = 4, binToX = 28)
## The same bins are thus used for each sub-set.

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.