vignettes/artMS_vignette.Rmd
artMS_vignette.RmdErrors or warnings? try to update the package first (resinstall) just in case a newer version is already available fixing the issue.
+Does the issue persist after reinstallation? Then, please, submit your error as a new issue at the official Github repository.
+Any other inquiries: artms.help@gmail.com
Analytical R Tools for Mass Spectrometry
(logical) if TRUE (default), prints out pdf
(logical) TRUE (default) print results tables
(logical) if TRUE, prints MSstats outputs (default is FALSE)
(logical) Default is FALSE.
+If TRUE, it returns a list of data frames with MSstats results, including:
comparisonResult: comparison results
ModelQC
FittedModel: fit model details
power: power calculations
sample_size: sample size estimations
(logical) TRUE (default) shows function messages
if (FALSE) { -artmsQuantification(yaml_config_file = "path/to/artms-ab-config.yaml") -} +diff --git a/docs/reference/artmsSILACtoLong.html b/docs/reference/artmsSILACtoLong.html index f97419a..47b3919 100644 --- a/docs/reference/artmsSILACtoLong.html +++ b/docs/reference/artmsSILACtoLong.html @@ -84,7 +84,7 @@ diff --git a/docs/reference/artmsSpectralCounts.html b/docs/reference/artmsSpectralCounts.html index 6e187cf..a1ec79d 100644 --- a/docs/reference/artmsSpectralCounts.html +++ b/docs/reference/artmsSpectralCounts.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/artmsVolcanoPlot.html b/docs/reference/artmsVolcanoPlot.html index 4926120..c1c8974 100644 --- a/docs/reference/artmsVolcanoPlot.html +++ b/docs/reference/artmsVolcanoPlot.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/artmsWriteConfigYamlFile.html b/docs/reference/artmsWriteConfigYamlFile.html index c9b2596..da7dcd0 100644 --- a/docs/reference/artmsWriteConfigYamlFile.html +++ b/docs/reference/artmsWriteConfigYamlFile.html @@ -85,7 +85,7 @@ diff --git a/docs/reference/artms_config.html b/docs/reference/artms_config.html index c511b68..3c52b9b 100644 --- a/docs/reference/artms_config.html +++ b/docs/reference/artms_config.html @@ -84,7 +84,7 @@ diff --git a/docs/reference/artms_data_corum_mito_database.html b/docs/reference/artms_data_corum_mito_database.html index f4474d1..0a8569d 100644 --- a/docs/reference/artms_data_corum_mito_database.html +++ b/docs/reference/artms_data_corum_mito_database.html @@ -88,7 +88,7 @@ diff --git a/docs/reference/artms_data_pathogen_LPN.html b/docs/reference/artms_data_pathogen_LPN.html index 932fc26..5ff6dbb 100644 --- a/docs/reference/artms_data_pathogen_LPN.html +++ b/docs/reference/artms_data_pathogen_LPN.html @@ -85,7 +85,7 @@ diff --git a/docs/reference/artms_data_pathogen_TB.html b/docs/reference/artms_data_pathogen_TB.html index 36b6ba0..b885bcf 100644 --- a/docs/reference/artms_data_pathogen_TB.html +++ b/docs/reference/artms_data_pathogen_TB.html @@ -85,7 +85,7 @@ diff --git a/docs/reference/artms_data_ph_config.html b/docs/reference/artms_data_ph_config.html index 1fa8c2c..4272997 100644 --- a/docs/reference/artms_data_ph_config.html +++ b/docs/reference/artms_data_ph_config.html @@ -83,7 +83,7 @@ diff --git a/docs/reference/artms_data_ph_contrast.html b/docs/reference/artms_data_ph_contrast.html index a39838d..b66f54a 100644 --- a/docs/reference/artms_data_ph_contrast.html +++ b/docs/reference/artms_data_ph_contrast.html @@ -84,7 +84,7 @@ diff --git a/docs/reference/artms_data_ph_evidence.html b/docs/reference/artms_data_ph_evidence.html index 04233d2..edd2b11 100644 --- a/docs/reference/artms_data_ph_evidence.html +++ b/docs/reference/artms_data_ph_evidence.html @@ -89,7 +89,7 @@ diff --git a/docs/reference/artms_data_ph_keys.html b/docs/reference/artms_data_ph_keys.html index b8eaa96..0f33ac1 100644 --- a/docs/reference/artms_data_ph_keys.html +++ b/docs/reference/artms_data_ph_keys.html @@ -86,7 +86,7 @@ diff --git a/docs/reference/artms_data_ph_msstats_modelqc.html b/docs/reference/artms_data_ph_msstats_modelqc.html index a008c22..b2c5248 100644 --- a/docs/reference/artms_data_ph_msstats_modelqc.html +++ b/docs/reference/artms_data_ph_msstats_modelqc.html @@ -83,7 +83,7 @@ diff --git a/docs/reference/artms_data_ph_msstats_results.html b/docs/reference/artms_data_ph_msstats_results.html index 4f27e86..63cfeaf 100644 --- a/docs/reference/artms_data_ph_msstats_results.html +++ b/docs/reference/artms_data_ph_msstats_results.html @@ -85,7 +85,7 @@ diff --git a/docs/reference/artms_data_randomDF.html b/docs/reference/artms_data_randomDF.html index fe9adc3..e12703f 100644 --- a/docs/reference/artms_data_randomDF.html +++ b/docs/reference/artms_data_randomDF.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/index.html b/docs/reference/index.html index 23fc4d6..b6905aa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@# Recommended +# artmsQuantification(yaml_config_file = "your-config-file.yaml") + +# Example to test this function using the example dataset available in artMS +# Step 1: Add evidence, keys, and contrast to configuration object +artms_data_ph_config$files$evidence <- artms_data_ph_evidence +artms_data_ph_config$files$keys <- artms_data_ph_keys +artms_data_ph_config$files$contrasts <- artms_data_ph_contrast + +# Step 2: Run the quantification step +quant_results <- artmsQuantification(yaml_config_file = artms_data_ph_config, + data_object = TRUE, + display_msstats = FALSE, + printPDF = FALSE, + printTables = FALSE) +#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>#>#># Check the list of data frames "quant_results". Nothing should be printed out.