README.md

In catrinanowakowski/ProcessIsodataOuts: What the Package Does (One Line, Title Case)

ProcessIsodataOuts

The goal of ProcessIsodataOuts is to read files from isodat, assign AA peak names, and then correct sample data based on standard runs. This package is still under development.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("catrinanowakowski/process_isodata_outs")

Example

This is a basic example which shows you how to solve a common problem:

library(ProcessIsodataOuts)


file_data <- c("C:/Thermo/Isodat NT/Global/User/Conflo IV Interface/Conflo IV Interface/Results/sherwood_220225_intercal_d13C/data")
AAStd_name <-  "772AAstd2"
AA_list <- c("Ala", "Gly", "Thr", "Ser", "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Glu", "Phe", "Tyr", "Lys")
C_N <- "C"
fl_nm <- "sherwood_220225_intercal_d13C"
order_AAs <- "Type" # "Type"
cyano <- "762cyano"
fish_muscle <- "763fish1"



# # ## A separate place where you want your final sample data to be stored:
file_save <- "C:/Users/EcoGeoChemLab/Documents"
# 
# ## Where this file you are using now lives:
# file_home <- "C:/Users/EcoGeoChemLab/isodat_processing"

## Carbon AA std files for your lab
file_save_AAstds_C <- "C:/Users/EcoGeoChemLab/Documents/AAStds_C"
## Carbon Labstd files for your lab
file_save_stds_C <- "C:/Users/EcoGeoChemLab/Documents/Stds_C"


## Nitrogen AA std files for your lab
file_save_AAstds_N <- "C:/Users/EcoGeoChemLab/Documents/AAStds_N"
## Nitrogen Labstd files for your lab
file_save_stds_N <- "C:/Users/EcoGeoChemLab/Documents/Stds_N"

##############################################################################
##############################################################################
## Code you shouldn't need to touch:

# file_sorc <- paste0(file_home, "/sorc") ## Where your source files are stored (These you should never have to touch, and should be the same if you are running normal data corrections or std test runs)

#######################
# source(paste0(file_sorc, "/process_CSIA_full_run.r"))     
outs <- process_CSIA_full_run()
#> Warning: package 'isoreader' was built under R version 4.1.2
#> 
#> Attaching package: 'isoreader'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_082121__772AAstd2_C_R1_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.54 secs
#> [1] 2
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_091541__772AAstd2_C_R2_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.20 secs
#> [1] 3
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_101003__772AAstd2_C_R3_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.29 secs
#> [1] 4
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_110424__772AAstd2_C_R4_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.24 secs
#> [1] 5
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_115835__762cyano_C_R1_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.20 secs
#> [1] 6
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_125244__762cyano_C_R2_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 7
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_134705__762cyano_C_R3_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 8
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_144129__762cyano_C_R4_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 9
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_153541__763fish1_C_R1_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.19 secs
#> [1] 10
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_162949__763fish1_C_R2_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.19 secs
#> [1] 11
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_172359__763fish1_C_R3_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 12
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_181810__763fish1_C_R4_330uLcut_100EA.dxf' from c...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 13
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_200830__772AAstd2_C_R5_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 14
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_210242__772AAstd2_C_R6_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 15
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_215704__772AAstd2_C_R7_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 16
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_225115__765chlor1_C_R1_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 17
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220225_234540__765chlor1_C_R2_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 18
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_003950__765chlor1_C_R3_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.19 secs
#> [1] 19
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_013359__765chlor1_C_R4_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.19 secs
#> [1] 20
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_022809__767AYS_C_R1_330uLcut_100EA.dxf' from cac...
#> Info: finished reading 1 files in 0.18 secs
#> [1] 21
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_032219__767AYS_C_R2_330uLcut_100EA.dxf' from cac...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 22
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_041629__767AYS_C_R3_330uLcut_100EA.dxf' from cac...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 23
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_051038__767AYS_C_R4_330uLcut_100EA.dxf' from cac...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 24
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_060648__772AAstd2_C_R8_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.16 secs
#> [1] 25
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_070110__772AAstd2_C_R9_330uLcut_100EA.dxf' from ...
#> Info: finished reading 1 files in 0.15 secs
#> [1] 26
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_075531__772AAstd2_C_R10_330uLcut_100EA.dxf' from...
#> Info: finished reading 1 files in 0.17 secs
#> [1] 27
#> Info: preparing to read 1 data files (all will be cached)...
#> Info: reading file '220226_084941__772AAstd2_C_R11_330uLcut_100EA.dxf' from...
#> Info: finished reading 1 files in 0.20 secs
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 22
#> [1] 1
#> [1] "Ala"
#> [1] 2
#> [1] "Gly"
#> [1] 3
#> [1] "Thr"
#> [1] 4
#> [1] "Ser"
#> [1] 5
#> [1] "Val"
#> [1] 6
#> [1] "Leu"
#> [1] 7
#> [1] "Ile"
#> [1] 8
#> [1] "NLeu"
#> [1] 9
#> [1] "Pro"
#> [1] 10
#> [1] "Asp"
#> [1] 11
#> [1] "Glu"
#> [1] 12
#> [1] "Phe"
#> [1] 13
#> [1] "Tyr"
#> [1] 14
#> [1] "Lys"
#> [1] 1
#> [1] "Ala"
#> [1] 2
#> [1] "Gly"
#> [1] 3
#> [1] "Thr"
#> [1] 4
#> [1] "Ser"
#> [1] 5
#> [1] "Val"
#> [1] 6
#> [1] "Leu"
#> [1] 7
#> [1] "Ile"
#> [1] 8
#> [1] "NLeu"
#> [1] 9
#> [1] "Pro"
#> [1] 10
#> [1] "Asp"
#> [1] 11
#> [1] "Glu"
#> [1] 12
#> [1] "Phe"
#> [1] 13
#> [1] "Tyr"
#> [1] 14
#> [1] "Lys"
#> [1] 1
#> [1] "Ala"
#> [1] 2
#> [1] "Gly"
#> [1] 3
#> [1] "Thr"
#> [1] 4
#> [1] "Ser"
#> [1] 5
#> [1] "Val"
#> [1] 6
#> [1] "Leu"
#> [1] 7
#> [1] "Ile"
#> [1] 8
#> [1] "NLeu"
#> [1] 9
#> [1] "Pro"
#> [1] 10
#> [1] "Asp"
#> [1] 11
#> [1] "Glu"
#> [1] 12
#> [1] "Phe"
#> [1] 13
#> [1] "Tyr"
#> [1] 14
#> [1] "Lys"
#> [1] 1
#> [1] "Ala"
#> [1] 2
#> [1] "Gly"
#> [1] 3
#> [1] "Thr"
#> [1] 4
#> [1] "Ser"
#> [1] 5
#> [1] "Val"
#> [1] 6
#> [1] "Leu"
#> [1] 7
#> [1] "Ile"
#> [1] 8
#> [1] "NLeu"
#> [1] 9
#> [1] "Pro"
#> [1] 10
#> [1] "Asp"
#> [1] 11
#> [1] "Glu"
#> [1] 12
#> [1] "Phe"
#> [1] 13
#> [1] "Tyr"
#> [1] 14
#> [1] "Lys"
#> Warning: Removed 12 rows containing missing values (geom_point).

#> Warning: Removed 16 rows containing missing values (geom_point).
#> Warning: Removed 3 rows containing missing values (geom_point).

#> Warning: Removed 3 rows containing missing values (geom_point).

#> Warning: Removed 12 rows containing missing values (geom_point).
#> Warning: Removed 16 rows containing missing values (geom_point).
#> Warning: Removed 3 rows containing missing values (geom_point).

#> Warning: Removed 3 rows containing missing values (geom_point).

all_fn_std_df <- outs$all_fn_std_df
all_fn_df <- outs$all_fn_df

catrinanowakowski/ProcessIsodataOuts documentation built on Jan. 29, 2023, 5:09 p.m.