This function can be used to manually adjust where certain blocks start or end after they have been defined with orbi_define_blocks() or orbi_define_blocks_for_dual_inlet() using either time or scan number.
The adjustments can be provided as vectors in the individual parameters or as a blocks_table - whichever is more convenient.
Note that adjusting blocks removes all block segmentation. Make sure to call orbi_segment_blocks() after adjusting block delimiters.
Usage
orbi_adjust_blocks(
dataset,
block = NULL,
in_filename = NULL,
shift_start_time.min = NULL,
shift_end_time.min = NULL,
shift_start_scan.no = NULL,
shift_end_scan.no = NULL,
set_start_time.min = NULL,
set_end_time.min = NULL,
set_start_scan.no = NULL,
set_end_scan.no = NULL,
blocks_table = NULL
)Arguments
- dataset
An aggregated dataset or a data frame of peaks (i.e. works directly after
orbi_identify_isotopocules()as well as with a tibble from orbi_get_data(peaks = everything()) or when reading from an IsoX file)- block
the block(s) for which to adjust the start and/or end, a single value or a vector for multiple adjustments. Note that blocks are numbered within each file.
- in_filename
the file(s) in which to adjust the block(s), a single value or a vector for multiple adjustments,
NA(the default if not provided) adjusts the block in all files that have it. This must be thefilenameof the file(s) as it appears in thedataset.- shift_start_time.min
if provided, the start time of the block will be shifted by this many minutes (use negative numbers to shift back)
- shift_end_time.min
if provided, the end time of the block will be shifted by this many minutes (use negative numbers to shift back)
- shift_start_scan.no
if provided, the start of the block will be shifted by this many scans (use negative numbers to shift back)
- shift_end_scan.no
if provided, the end of the block will be shifted by this many scans (use negative numbers to shift back)
- set_start_time.min
if provided, sets the start time of the block as close as possible to this time
- set_end_time.min
if provided, sets the end time of the block as close as possible to this time
- set_start_scan.no
if provided, sets the start of the block to this scan number (scan must exist in the
dataset)- set_end_scan.no
if provided, sets the end of the block to this scan number (scan must exist in the
dataset)- blocks_table
alternative to the individual parameters: a data frame with the column
blockand any of the columnsin_filename,shift_start_time.min,shift_end_time.min,shift_start_scan.no,shift_end_scan.no,set_start_time.min,set_end_time.min,set_start_scan.noandset_end_scan.no, one row per adjustment. Any other columns are ignored. If provided, the individual parameters are not used.
Value
A data frame (tibble) with block limits altered according to the provided start/end change parameters. Any data that is no longer part of the original block will be marked with the value of orbi_get_option("data_type_unused"). Any previously applied segmentation of the adjusted blocks' files will be discarded (segment column set to NA) to avoid unintended side effects.
Details
Each adjustment can change the start of a block (with only one of shift_start_time.min, shift_start_scan.no, set_start_time.min, or set_start_scan.no) and/or the end of a block (with only one of shift_end_time.min, shift_end_scan.no, set_end_time.min, or set_end_scan.no). The adjustments are applied in the order they are provided.
Examples
fpath <- system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")
df <- orbi_read_isox(file = fpath) |>
orbi_simplify_isox() |>
orbi_define_blocks_for_dual_inlet(
ref_block_time.min = 0.5,
change_over_time.min = 0.1
)
#> ✔ [120ms] orbi_read_isox() loaded 5.18k peaks for 1 compound (NO3-) with 6
#> isotopocules (15N, 17O, 18O, 15N18O, 17O18O, and 18O18O) from
#> testfile_dual_inlet.isox
#> ✔ [4ms] orbi_simplify_isox() kept columns filepath, filename, scan.no,
#> time.min, compound, isotopocule, ions.incremental, tic, and it.ms
#> ✔ [26ms] orbi_define_blocks_for_dual_inlet() identified 6 blocks (3 ref, 3 sam)
#> in data from 1 file
# shift the start of block 1 by 6 seconds in all files
df |> orbi_adjust_blocks(block = 1, shift_start_time.min = 0.1)
#> ✔ [37ms] orbi_adjust_blocks() adjusted 1 block in 1 file
#> → block 1 in 20220125_01: moved start from scan 1 (300ms) to 29 (6.4s)
#> # A tibble: 5,184 × 14
#> filepath filename scan.no time.min compound isotopocule ions.incremental
#> <chr> <fct> <int> <dbl> <fct> <fct> <dbl>
#> 1 /home/runner… 2022012… 1 0.005 NO3- 15N 74181.
#> 2 /home/runner… 2022012… 1 0.005 NO3- 17O 23132.
#> 3 /home/runner… 2022012… 1 0.005 NO3- 18O 171489.
#> 4 /home/runner… 2022012… 1 0.005 NO3- 15N18O 746.
#> 5 /home/runner… 2022012… 1 0.005 NO3- 17O18O 122.
#> 6 /home/runner… 2022012… 1 0.005 NO3- 18O18O 405.
#> 7 /home/runner… 2022012… 2 0.008 NO3- 15N 73402.
#> 8 /home/runner… 2022012… 2 0.008 NO3- 17O 23859.
#> 9 /home/runner… 2022012… 2 0.008 NO3- 18O 172534.
#> 10 /home/runner… 2022012… 2 0.008 NO3- 15N18O 759.
#> # ℹ 5,174 more rows
#> # ℹ 7 more variables: tic <dbl>, it.ms <dbl>, data_group <int>, block <int>,
#> # block_name <chr>, data_type <chr>, segment <int>
# several adjustments at once
df |> orbi_adjust_blocks(
block = c(1, 2),
shift_start_time.min = c(0.1, 0.05),
shift_end_time.min = c(NA, -0.05)
)
#> ✔ [91ms] orbi_adjust_blocks() adjusted 2 blocks in 1 file
#> → block 1 in 20220125_01: moved start from scan 1 (300ms) to 29 (6.4s)
#> → block 2 in 20220125_01: moved start from scan 167 (36.1s) to 181 (39.1s)
#> → block 2 in 20220125_01: moved end from scan 277 (59.8s) to 262 (56.6s)
#> # A tibble: 5,184 × 14
#> filepath filename scan.no time.min compound isotopocule ions.incremental
#> <chr> <fct> <int> <dbl> <fct> <fct> <dbl>
#> 1 /home/runner… 2022012… 1 0.005 NO3- 15N 74181.
#> 2 /home/runner… 2022012… 1 0.005 NO3- 17O 23132.
#> 3 /home/runner… 2022012… 1 0.005 NO3- 18O 171489.
#> 4 /home/runner… 2022012… 1 0.005 NO3- 15N18O 746.
#> 5 /home/runner… 2022012… 1 0.005 NO3- 17O18O 122.
#> 6 /home/runner… 2022012… 1 0.005 NO3- 18O18O 405.
#> 7 /home/runner… 2022012… 2 0.008 NO3- 15N 73402.
#> 8 /home/runner… 2022012… 2 0.008 NO3- 17O 23859.
#> 9 /home/runner… 2022012… 2 0.008 NO3- 18O 172534.
#> 10 /home/runner… 2022012… 2 0.008 NO3- 15N18O 759.
#> # ℹ 5,174 more rows
#> # ℹ 7 more variables: tic <dbl>, it.ms <dbl>, data_group <int>, block <int>,
#> # block_name <chr>, data_type <chr>, segment <int>
# the same via a blocks table
df |> orbi_adjust_blocks(
blocks_table = tibble::tibble(
block = c(1, 2),
shift_start_time.min = c(0.1, 0.05),
shift_end_time.min = c(NA, -0.05)
)
)
#> ✔ [93ms] orbi_adjust_blocks() adjusted 2 blocks in 1 file
#> → block 1 in 20220125_01: moved start from scan 1 (300ms) to 29 (6.4s)
#> → block 2 in 20220125_01: moved start from scan 167 (36.1s) to 181 (39.1s)
#> → block 2 in 20220125_01: moved end from scan 277 (59.8s) to 262 (56.6s)
#> # A tibble: 5,184 × 14
#> filepath filename scan.no time.min compound isotopocule ions.incremental
#> <chr> <fct> <int> <dbl> <fct> <fct> <dbl>
#> 1 /home/runner… 2022012… 1 0.005 NO3- 15N 74181.
#> 2 /home/runner… 2022012… 1 0.005 NO3- 17O 23132.
#> 3 /home/runner… 2022012… 1 0.005 NO3- 18O 171489.
#> 4 /home/runner… 2022012… 1 0.005 NO3- 15N18O 746.
#> 5 /home/runner… 2022012… 1 0.005 NO3- 17O18O 122.
#> 6 /home/runner… 2022012… 1 0.005 NO3- 18O18O 405.
#> 7 /home/runner… 2022012… 2 0.008 NO3- 15N 73402.
#> 8 /home/runner… 2022012… 2 0.008 NO3- 17O 23859.
#> 9 /home/runner… 2022012… 2 0.008 NO3- 18O 172534.
#> 10 /home/runner… 2022012… 2 0.008 NO3- 15N18O 759.
#> # ℹ 5,174 more rows
#> # ℹ 7 more variables: tic <dbl>, it.ms <dbl>, data_group <int>, block <int>,
#> # block_name <chr>, data_type <chr>, segment <int>