ri_data_extract {TargetSearch} | R Documentation

## Extract peak data from a RI file

### Description

A convenient function to extract peak data from a RI file. This function is mostly intended for debugging purposes, for example, when a given peak is not found within a expected time range (which could be because a faulty retention time correction). The arguments of this function are similar as those of the `ncdf4_data_extract` function.

### Usage

    ri_data_extract(RIfile, massValues, timeRange, useRT = FALSE, ...)

### Arguments

`RIfile` | A path to a RI file format (binary or text).
`massValues` | A numeric vector representing m/z values. The values will be converted to integers internally.
`timeRange` | A numeric vector of even length, or, a two-column matrix. This parameter represents the lower and upper time limits. See details below.
`useRT` | Logical. If `TRUE`, the time range is in seconds, otherwise if `FALSE` (default), the time range is in retention time index units (`TRUE`).
`...` | Extra parameters passed to internal functions. Currently, only the `columns` parameter is used for text-format RI files. This, however, should not be necessary. See also `text2bin`.

### Details

The function takes a RI file generated by `TargetSearch` (binary or text works) and extracts all the peaks detected of given m/z ion traces in a given time range. The time range can be in seconds or arbitrary retention time index units.

The parameter `timeRange` can be either a numeric vector of even length or a two-column matrix. If it is a matrix, the first column represent the lower bounds while the second the upper ones. If it is a vector, it must have at least two elements, which in this case represent the lower and upper limits, or if longer, it will be coerced to matrix internally (Important: the values are filled by columns). In any case, the number of rows of the (coerced) matrix must divide the length of the `massValues` parameter, such that each row corresponds to a time range for each m/z value. This is done so the ranges can be recycled.

The output is simply a four column matrix in which a row is a peak of a given ion trace at a retention time (index). The output is always a matrix even if no peaks are found, in which case the number of rows is zero.

### Value

A four column matrix with column names described below. Each row represents a peak in the specified time range. Potentially, there could be zero rows if no peaks are found.

- `RI` retention time index of the peak.

- `RT` retention time.

- `Intensity` peak height intensity

- `mz` the m/z of the peak

### Note

This function is intended to be used internally or by advances users. It can be used for debugging when `TargetSearch` fails to find a peak.

See also the function `FindAllPeaks` which offers a similar functionality but with different input parameters.

### Author(s)

Alvaro Cuadros-Inostroza

### See Also

`text2bin`, `ncdf4_data_extract`, `FindAllPeaks`, `FindPeaks`

### Examples

    require(TargetSearchData)
    path <- file.path(find.package("TargetSearchData"), "gc-ms-data")
    rifile <- dir(path, pattern="RI_", full=TRUE)[1]

    # extract peak data for m/z 116 and 117 in time range 180 - 220 seconds
    data <- ri_data_extract(rifile, c(116, 117), c(180, 220), useRT=TRUE)

    # same but using Retention Time Index
    data <- ri_data_extract(rifile, c(116, 117), c(205000, 228000), useRT=FALSE)

    # different time ranges for each m/z
    trange <- c(180, 240, 280, 190, 250, 290)
    data <- ri_data_extract(rifile, c(116, 144, 147), trange, useRT=TRUE)

    # Note: the range definition above is equivalent to
    trange <- cbind(c(180,240,280), c(190, 250, 290))

[Package TargetSearch version 1.48.0 Index]