Extract expression_data from mass_dataset
Extract sample information.
Extract variable information.
Extract variable information.
Extract variable information note.
Extract sample information note.
Extract process information
Extract ms2 data
extract_expression_data(object)
extract_sample_info(object)
extract_variable_info(object, with_expression_data = FALSE)
extract_annotation_table(object, with_expression_data = FALSE)
extract_variable_info_note(object)
extract_sample_info_note(object)
extract_process_info(object)
extract_ms2_data(object)
# S4 method for mass_dataset
sample_info(object)
# S4 method for mass_dataset
expression_data(object)
# S4 method for mass_dataset
variable_info(object)
# S4 method for mass_dataset
process_info(object)
# S4 method for mass_dataset
ms2_data(object)
# S4 method for mass_dataset
sample_info_note(object)
# S4 method for mass_dataset
variable_info_note(object)
# S4 method for mass_dataset
annotation_table(object)(required) mass_dataset class object
should the extracted annotation table with expression data.
A data frame (expression_data).
A data frame (sample_info).
A data frame (variable_info).
A data frame (annotation_table).
A data frame (variable_info_note).
A data frame (sample_info_note).
A list of tidymass_parameter.
A ms2_data class object.
A data.frame (sample_info)
A data.frame (expression_data)
A data.frame (variable_info)
A list of tidymass_parameter class objects
A ms2_data class object.
A data.frame (sample_info_note)
A data.frame (variable_info_note)
A data.frame (annotation_table)
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
variable_info = variable_info,
sample_info = sample_info
)
expression_data2 =
extract_expression_data(object = object)
head(expression_data2)
#> Blank_3 Blank_4 QC_1 QC_2 PS4P1 PS4P2 PS4P3
#> M136T55_2_POS NA NA 1857924.8 1037763.8 1494436.1 3496912.1 1959179
#> M79T35_POS NA NA 2821550.2 1304875.3 2471336.1 3333582.7 2734244
#> M307T548_POS NA NA 410387.6 273687.8 288590.2 137297.5 NA
#> M183T224_POS NA NA NA NA NA 5059068.1 5147422
#> M349T47_POS NA NA 8730104.8 4105598.5 5141073.2 8424315.6 7896633
#> M182T828_POS 3761893 2572593 NA 3662819.1 5700534.8 4600172.4 5557015
#> PS4P4
#> M136T55_2_POS 1005418.8
#> M79T35_POS 3361452.3
#> M307T548_POS 271318.3
#> M183T224_POS NA
#> M349T47_POS 6441449.0
#> M182T828_POS 4433034.2
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
sample_info2 =
extract_sample_info(object = object)
head(sample_info2)
#> sample_id injection.order class group
#> 1 Blank_3 1 Blank Blank
#> 2 Blank_4 2 Blank Blank
#> 3 QC_1 3 QC QC
#> 4 QC_2 4 QC QC
#> 5 PS4P1 5 Subject Subject
#> 6 PS4P2 6 Subject Subject
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
variable_info2 =
extract_variable_info(object = object)
head(variable_info2)
#> variable_id mz rt
#> 1 M136T55_2_POS 136.06140 54.97902
#> 2 M79T35_POS 79.05394 35.36550
#> 3 M307T548_POS 307.14035 547.56641
#> 4 M183T224_POS 183.06209 224.32777
#> 5 M349T47_POS 349.01584 47.00262
#> 6 M182T828_POS 181.99775 828.35712
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
annotation_table =
extract_annotation_table(object = object)
head(annotation_table)
#> data frame with 0 columns and 0 rows
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
test =
extract_variable_info_note(object = object)
head(test)
#> name meaning
#> 1 variable_id variable_id
#> 2 mz mz
#> 3 rt rt
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
test =
extract_sample_info_note(object = object)
head(test)
#> name meaning
#> 1 sample_id sample_id
#> 2 injection.order injection.order
#> 3 class class
#> 4 group group
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
object
#> --------------------
#> massdataset version: 1.0.27
#> --------------------
#> 1.expression_data:[ 1000 x 8 data.frame]
#> 2.sample_info:[ 8 x 4 data.frame]
#> 8 samples:Blank_3 Blank_4 QC_1 ... PS4P3 PS4P4
#> 3.variable_info:[ 1000 x 3 data.frame]
#> 1000 variables:M136T55_2_POS M79T35_POS M307T548_POS ... M232T937_POS M301T277_POS
#> 4.sample_info_note:[ 4 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> --------------------
#> Processing information
#> 1 processings in total
#> create_mass_dataset ----------
#> Package Function.used Time
#> 1 massdataset create_mass_dataset() 2023-10-01 09:40:58
extract_process_info(object)
#> $create_mass_dataset
#> --------------------
#> pacakge_name: massdataset
#> function_name: create_mass_dataset()
#> time: 2023-10-01 09:40:58.118454
#> parameters:
#> no : no
#>
data("expression_data")
data("sample_info")
data("variable_info")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info,
)
test =
extract_ms2_data(object = object)