Description Usage Arguments Details Value Examples

Creates a data structure encapsulating the mass spectrometry intensity readings as well as identifying information

1 |

`mass_spec` |
Either a For example, suppose that a collection of mass spectrometry intensity
observations has provided data for 50 fractions across 20,000
mass-to-charge values. Then the input for |

`mtoz` |
A vector of either length 1 or length equal to the number of mass-to-charge values for which mass spectrometry data was collected, and which helps identify the mass-to-charge values for this data in one of several ways. One way to provide the information is to provide a numeric vector where
each entry provides the mass-to-charge value for a corresponding row of
mass spectrometry data. Then the A second way is to provide a single number which specifies the column
index in the A third way is provide a single character string which provides the
column name in the |

`charge` |
The information for the |

`ms_inten` |
Either |

Since the mass spectrometry data could conceivably be available to
the researcher in a variety forms, this function attempts to provide a
uniform data structure for encapsulating this information. It is the
fundamental data structure containing the mass spectrometry data used
internally by the `filterMS`

and `rankEN`

routines. The
external interface for `msDat`

is provided to the user so that
specifying the mass spectrometry information can be made in a distinct
step from performing statistical analyses, which it is hoped makes
interfaces for the downstream analysis routines simpler and more
intuitive to use.

Returns an object of class `msDat`

. This class is a `list`

with elements described below. The class is equipped with a `print`

and `extractMS`

function.

`ms`

A

`matrix`

containing mass spectrometry intensity readings. Each column provides the mass spectrometry values for a given fraction, and each row provides the mass spectrometry values for a given mass-to-charge ratio value across the fractions.`mtoz`

A vector with length equal to the number of mass-to-charge values provided in the mass spectrometry data, such that the

`k`

-th entry in the vector provides the mass-to-charge value for the`k`

-th row of mass spectrometry data`chg`

A vector with length equal to the number of mass-to-charge values provided in the mass spectrometry data, such that the

`k`

-th entry in the vector provides the charge information for the`k`

-th row of mass spectrometry data

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ```
# Load mass spectrometry data
data(mass_spec)
# Convert mass_spec from a data.frame to an msDat object
ms <- msDat(mass_spec = mass_spec,
mtoz = "m/z",
charge = "Charge",
ms_inten = c(paste0("_", 11:43), "_47"))
# Dimension of the data
dim(ms)
# Print the first few rows and columns
ms[1:5, 1:2]
# Let's change the fraction names to something more concise
colnames(ms) <- c(paste0("frac", 11:43), "frac47")
# Print the first few rows and columns with the new fraction names
ms[1:5, 1:8]
# Suppose there are some m/z levels that we wish to remove
ms <- ms[-c(2, 4), ]
# Print the first few rows and columns after removing rows 2 and 4
ms[1:5, 1:8]
# Suppose that there was an instrumentation error and that we need to change
# some values
ms[1, paste0("frac", 12:17)] <- c(55, 57, 62, 66, 71, 79)
# Print the first few rows and columns after changing some of the values in
# the first row
ms[1:5, 1:10]
``` |

dpritchLibre/PepSAVIms documentation built on Oct. 1, 2017, 4:14 a.m.

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