Data import and export

library(tidyverse)
peak_table_pos = readr::read_csv("feature_table/Peak_table_pos.csv")
#> Rows: 1612 Columns: 39
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (1): variable_id
#> dbl (38): mz, rt, bl20210902_10, bl20210902_11, bl20210902_13, bl20210902_14...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
peak_table_neg = readr::read_csv("feature_table/Peak_table_neg.csv")
#> Rows: 5486 Columns: 39
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (1): variable_id
#> dbl (38): mz, rt, X20210902_neg04, X20210902_neg05, X20210902_neg06, X202109...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

sample_info_pos = readr::read_csv("feature_table/sample_info_pos.csv")
#> Rows: 36 Columns: 4
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sample_id, class, group
#> dbl (1): injection.order
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
sample_info_neg = readr::read_csv("feature_table/sample_info_neg.csv")
#> Rows: 36 Columns: 4
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sample_id, class, group
#> dbl (1): injection.order
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

expression_data_pos = 
  peak_table_pos %>% 
  dplyr::select(-c(variable_id:rt)) %>% 
  as.data.frame()

variable_info_pos = 
  peak_table_pos %>% 
  dplyr::select(variable_id:rt) %>% 
  as.data.frame()

rownames(expression_data_pos) = variable_info_pos$variable_id

expression_data_neg = 
  peak_table_neg %>% 
  dplyr::select(-c(variable_id:rt)) %>% 
  as.data.frame()

variable_info_neg = 
  peak_table_neg %>% 
  dplyr::select(variable_id:rt) %>% 
  as.data.frame()

rownames(expression_data_neg) = variable_info_neg$variable_id

colnames(expression_data_pos) == sample_info_pos$sample_id
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
colnames(expression_data_neg) == sample_info_neg$sample_id
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE

expression_data_pos = 
  expression_data_pos[,sample_info_pos$sample_id]

expression_data_neg = 
  expression_data_neg[,sample_info_neg$sample_id]

colnames(expression_data_pos) == sample_info_pos$sample_id
#>  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [31] TRUE TRUE TRUE TRUE TRUE TRUE
colnames(expression_data_neg) == sample_info_neg$sample_id
#>  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [31] TRUE TRUE TRUE TRUE TRUE TRUE

library(massdataset)

object_pos =
  create_mass_dataset(
    expression_data = expression_data_pos,
    sample_info = sample_info_pos,
    variable_info = variable_info_pos
  )
  
object_pos
#> -------------------- 
#> massdataset version: 1.0.12 
#> -------------------- 
#> 1.expression_data:[ 1612 x 36 data.frame]
#> 2.sample_info:[ 36 x 4 data.frame]
#> 3.variable_info:[ 1612 x 3 data.frame]
#> 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 (extract_process_info())
#> 1 processings in total
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-08-07 19:21:48

object_neg =
  create_mass_dataset(
    expression_data = expression_data_neg,
    sample_info = sample_info_neg,
    variable_info = variable_info_neg
  )
  
object_neg
#> -------------------- 
#> massdataset version: 1.0.12 
#> -------------------- 
#> 1.expression_data:[ 5486 x 36 data.frame]
#> 2.sample_info:[ 36 x 4 data.frame]
#> 3.variable_info:[ 5486 x 3 data.frame]
#> 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 (extract_process_info())
#> 1 processings in total
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-08-07 19:21:48

save(object_pos, file = "feature_table/object_pos")
save(object_neg, file = "feature_table/object_neg")

export_mass_dataset(object = object_pos,
                    file_type = "xlsx",
                    path = "demo_data_pos")