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Merge pull request #97 from uparma/mx/merge_analytical_replicates
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* added merge_analytical_replicates style
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@tristan-ranff
tristan-ranff authored Aug 12, 2022
2 parents 4742d1d + d945221 commit bdb4efc
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Showing 2 changed files with 99 additions and 2 deletions.
77 changes: 75 additions & 2 deletions jsons/parameters.json
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Expand Up @@ -5762,7 +5762,9 @@
"default_value": "CTRL",
"description": "Experimental condition as required by experimental_setup collection.",
"key_translations": {
"filter_nonbiological_ions_style_1": "condition",
"flash_lfq_style_1": "Condition",
"merge_analytical_replicates_style_1": "condition",
"pw-stats_style_1": "Condition",
"ursgal_style_1": "exp-setup_condition"
},
Expand All @@ -5778,7 +5780,9 @@
"default_value": "FileName",
"description": "File Name as required by experimental_setup collection.",
"key_translations": {
"filter_nonbiological_ions_style_1": "filename",
"flash_lfq_style_1": "FileName",
"merge_analytical_replicates_style_1": "filename",
"pw-stats_style_1": "FileName",
"ursgal_style_1": "exp-setup_filename"
},
Expand Down Expand Up @@ -5821,11 +5825,61 @@
"value_translations": {},
"value_type": "str"
},
{
"default_value": 1,
"description": "MS run index as required by experimental_setup collection.",
"key_translations": {
"filter_nonbiological_ions_style_1": "ms_run_index",
"merge_analytical_replicates_style_1": "ms_run_index",
"ursgal_style_1": "exp-setup_ms_run_index"
},
"name": "exp-setup_ms_run_index",
"tag": [
"experiment_setup"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "int"
},
{
"default_value": 0,
"description": "Sample index as required by experimental_setup collection. Sample Index 0 is typically used by QC samples.",
"key_translations": {
"filter_nonbiological_ions_style_1": "sample_index",
"merge_analytical_replicates_style_1": "sample_index",
"ursgal_style_1": "exp-setup_sample_index"
},
"name": "exp-setup_sample_index",
"tag": [
"experiment_setup"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "int"
},
{
"default_value": null,
"description": "Sample type as required by experimental_setup collection.",
"key_translations": {
"filter_nonbiological_ions_style_1": "sample_type",
"merge_analytical_replicates_style_1": "sample_type",
"ursgal_style_1": "exp-setup_sample_type"
},
"name": "exp-setup_sample_type",
"tag": [
"experiment_setup"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": 1,
"description": "Technical replicate ID as required by experimental_setup collection.",
"key_translations": {
"filter_nonbiological_ions_style_1": "analytical_replicate",
"flash_lfq_style_1": "Techrep",
"merge_analytical_replicates_style_1": "analytical_replicate",
"pw-stats_style_1": "TechnicalReplicate",
"ursgal_style_1": "exp-setup_technical_replicate"
},
Expand All @@ -5842,7 +5896,9 @@
"description": " ",
"is_parameter_collection": true,
"key_translations": {
"filter_nonbiological_ions_style_1": "metadata",
"flash_lfq_style_1": "experiment_setup\nFormat:\n{\"1\": {\"FileName\": <filename as in identfile>, \"Condition\":<str>, \"Biorep\": <int>, \"Fraction\": <int>, \"Techrep\": <int>},\n\"2\": ....\n}\n",
"merge_analytical_replicates_style_1": "metadata",
"pw-stats_style_1": "experimental_design",
"ursgal_style_1": "experiment_setup"
},
Expand Down Expand Up @@ -6073,8 +6129,9 @@
},
{
"default_value": 0.1,
"description": "fold-change cutoff for Bayesian protein fold-change analysis",
"description": "fold-change cutoff for fold-change analysis",
"key_translations": {
"filter_nonbiological_ions_style_1": "cv_ratio",
"flash_lfq_style_1": "--fcc",
"ursgal_style_1": "fold_change_cutoff"
},
Expand Down Expand Up @@ -6132,10 +6189,12 @@
},
{
"default_value": 0.1,
"description": "fraction of non-NA data points in which ion was detected in current scan window to compute TIC correlation",
"description": "fraction of non-NA data points in which ions were detected",
"key_translations": {
"align_files_dbscan_style_1": "min_scans_frac",
"align_scans_dbscan_style_1": "min_scans_frac",
"correct_instrument_drift_style_1": "min_cmatrix_ions_frac",
"filter_nonbiological_ions_style_1": "min_cmatrix_ions_frac",
"ursgal_style_1": "fraction_detected_ions"
},
"name": "fraction_detected_ions",
Expand Down Expand Up @@ -9890,6 +9949,20 @@
"value_translations": {},
"value_type": "int"
},
{
"default_value": 5,
"description": "min absolute number of non-NA data points in which ions were detected",
"key_translations": {
"correct_instrument_drift_style_1": "min_cmatrix_ions",
"filter_nonbiological_ions_style_1": "min_cmatrix_ions",
"ursgal_style_1": "min_number_detected_ions"
},
"name": "min_number_detected_ions",
"tag": [],
"triggers_rerun": true,
"value_translations": {},
"value_type": "int"
},
{
"default_value": 2,
"description": " Min number of matched isotopologues to consider for quantification ",
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24 changes: 24 additions & 0 deletions jsons/styles.json
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Original file line number Diff line number Diff line change
Expand Up @@ -654,5 +654,29 @@
"1.0.0"
],
"reference": "Ursgal2 Team"
},
{
"style": "merge_analytical_replicates_style_1",
"name": "merge_analytical_replicates_style_1",
"versions": [
"1.0.0"
],
"reference": "Ursgal2 Team"
},
{
"style": "filter_nonbiological_ions_style_1",
"name": "filter_nonbiological_ions_style_1",
"versions": [
"1.0.0"
],
"reference": "Ursgal2 Team"
},
{
"style": "correct_instrument_drift_style_1",
"name": "correct_instrument_drift_style_1",
"versions": [
"1.0.0"
],
"reference": "Ursgal2 Team"
}
]

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