Description Usage Arguments Details Value See Also Examples

View source: R/calculate_kinetics.R

Calculate kinetics of the hydrogen-deuteration exchange for given peptide.

1 2 3 4 5 6 7 8 9 10 11 |

`dat` |
dat data read by |

`protein` |
protein value for chosen peptide |

`sequence` |
sequence of the peptide for which the kinetics is calculated |

`state` |
state of given sequence |

`start` |
end of given sequence |

`end` |
end of given sequence |

`time_in` |
time in for experimental calculations |

`time_out` |
time out for experimental calculations |

`deut_part` |
percentage of deuterium the protein was exposed to, value in range [0, 1] |

The function calculates deuteration data for all available data points
for given peptide.
All four variants (relative & theoretical combinations) of deuteration computations
are supported. Manual correction of percentage of deuterium the protein was exposed
to during the exchange in theoretical calculations is provided.
To visualize obtained data we recommend using `plot_kinetics`

function.
The first version doesn't support filled Modification and Fragment columns.

data frame with deuteration calculated for all the data points
between time_in and time_out.
The chosen time point for which deuteration in all four variants is calculated
is available in column 'time_chosen'. The rest of
the returned structure is equivalent to structure returned by
`calculate_state_deuteration`

.

`read_hdx`

`calculate_state_deuteration`

`plot_kinetics`

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 33 34 35 36 37 38 39 40 | ```
# load example data
dat <- read_hdx(system.file(package = "HaDeX",
"HaDeX/data/KD_180110_CD160_HVEM.csv"))
# calculate data for sequence INITSSASQEGTRLN in state CD160
(kin1 <- calculate_kinetics(dat,
protein = "db_CD160",
sequence = "INITSSASQEGTRLN",
state = "CD160",
start = 1,
end = 15,
time_in = 0.001,
time_out = 1440))
# calculate data for sequence INITSSASQEGTRLN in state CD160_HVEM
(kin2 <- calculate_kinetics(dat,
protein = "db_CD160",
sequence = "INITSSASQEGTRLN",
state = "CD160_HVEM",
start = 1,
end = 15,
time_in = 0.001,
time_out = 1440))
# load extra libraries
library(dplyr)
library(ggplot2)
# plot example - experimental and relative
bind_rows(kin1, kin2) %>%
plot_kinetics(theoretical = FALSE,
relative = TRUE) +
labs(title = "Kinetic plot for INITSSASQEGTRLN")
# plot example - theoretical and absolute
bind_rows(kin1, kin2) %>%
plot_kinetics(theoretical = TRUE,
relative = FALSE) +
labs(title = "Theoretical kinetics plot for INITSSASQEGTRLN")
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.