Update documentation and comments

calico · May 16, 2024 · 5ef645e · 5ef645e
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Showing 13 changed files with 20 additions and 89 deletions.
diff --git a/R/mutate_mzroll_list.R b/R/mutate_mzroll_list.R
@@ -999,6 +999,11 @@ fit_lm <- function (groupData,
   # Compute corrected values
   lm_apply <- lm_data %>%
     dplyr::mutate(median_value = median(.data$val_var, na.rm = T)) %>%
+
+    # Assign new normalized variable norm_peak_varname:
+    # Predict values from linear fit are subtracted from quant_peak_varname,
+    # which centers the data around zero
+    # Median value from quant_peak_varname is added back to maintain abundance value
     dplyr::mutate(`:=`(!!rlang::sym(norm_peak_varname), 
                        .data$val_var - .env$predict(lm_model, newdata = lm_data) + .data$median_value)) %>%
                     dplyr::mutate(lm_estimate = summary(.env$lm_model)$coefficient[2,1]) %>%

diff --git a/man/collapse_injections.Rd b/man/collapse_injections.Rd
diff --git a/man/collapse_metabolites.Rd b/man/collapse_metabolites.Rd
diff --git a/man/diffex_mzroll.Rd b/man/diffex_mzroll.Rd
diff --git a/man/filter_groupIds.Rd b/man/filter_groupIds.Rd
diff --git a/man/find_pathway_enrichments.Rd b/man/find_pathway_enrichments.Rd
diff --git a/man/floor_peaks.Rd b/man/floor_peaks.Rd
diff --git a/man/merge_compounds_tbl.Rd b/man/merge_compounds_tbl.Rd
diff --git a/man/merge_samples_tbl.Rd b/man/merge_samples_tbl.Rd
diff --git a/man/normalize_peaks.Rd b/man/normalize_peaks.Rd
diff --git a/man/plot_barplot.Rd b/man/plot_barplot.Rd
diff --git a/man/plot_compare_injection.Rd b/man/plot_compare_injection.Rd
diff --git a/man/test_mzroll_list.Rd b/man/test_mzroll_list.Rd