Get Some Information of a mass_dataset Object

These functions returns the information of a mass_dataset object.

get_sample_number(object)

get_variable_number(object)

get_sample_id(object)

get_variable_id(object)

get_mv_number(
  object,
  by = c("total", "sample", "variable"),
  show_by = c("number", "percentage")
)

Arguments

object

A mass_dataset object.

by

A character string specifying how to count missing values. Options are "total", "sample", or "variable". Default is "total".

show_by

A character string specifying the format to show the result. Options are "number" or "percentage". Default is "number".

Author

Xiaotao Shen shenxt1990@outlook.com

Examples

###get_sample_number
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,
  )
 get_sample_number(object = object)
#> [1] 8
###get_variable_number
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,
  )
 get_variable_number(object = object)
#> [1] 1000
###get_sample_id
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,
  )
 get_sample_id(object = object)
#> [1] "Blank_3" "Blank_4" "QC_1"    "QC_2"    "PS4P1"   "PS4P2"   "PS4P3"  
#> [8] "PS4P4"  
###get_variable_id
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,
  )
 head(get_variable_id(object = object))
#> [1] "M136T55_2_POS" "M79T35_POS"    "M307T548_POS"  "M183T224_POS" 
#> [5] "M349T47_POS"   "M182T828_POS" 
###get_mv_number
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: 1.0.28 
#> -------------------- 
#> 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 23:24:29
head(get_variable_id(object = object))
#> [1] "M136T55_2_POS" "M79T35_POS"    "M307T548_POS"  "M183T224_POS" 
#> [5] "M349T47_POS"   "M182T828_POS" 
get_mv_number(object)
#> [1] 3829
get_mv_number(object, by = "sample")
#> Blank_3 Blank_4    QC_1    QC_2   PS4P1   PS4P2   PS4P3   PS4P4 
#>     682     702     397     381     424     427     405     411 
head(get_mv_number(object, by = "variable", "percentage"))
#> M136T55_2_POS    M79T35_POS  M307T548_POS  M183T224_POS   M349T47_POS 
#>         0.250         0.250         0.375         0.750         0.250 
#>  M182T828_POS 
#>         0.125