Package index • glyclean

Automactic Processing

auto_clean(): Automatic Data Preprocessing
auto_aggregate(): Automatic Aggregation
auto_impute(): Automatic Imputation
auto_normalize(): Automatic Normalization
auto_remove(): Automatic Removing Variables
auto_correct_batch_effect(): Automatic Batch Correction

Aggregation

aggregate() glyclean_aggregate(<glyexp_experiment>) glyclean_aggregate(<default>): Aggregate Data

Normalization

normalize_loesscyc(): LoessCyc Normalization
normalize_loessf(): LoessF Normalization
normalize_median(): Median Normalization
normalize_median_abs(): Absolute Median Normalization
normalize_median_quotient(): Median Quotient Normalization
normalize_quantile(): Quantile Normalization
normalize_rlr(): Robust Linear Regression Normalization
normalize_rlrma(): Robust Linear Regression with Median Adjustment Normalization
normalize_rlrmacyc(): Robust Linear Regression with Median Adjustment and Cyclic Normalization
normalize_total_area(): Total Area Normalization
normalize_vsn(): Variance Stabilizing Normalization

Imputation

impute_bpca(): BPCA Imputation
impute_fw_knn(): Feature-wise KNN Imputation
impute_half_sample_min(): Half Sample Minimum Imputation
impute_min_prob(): Minimum Probability Imputation
impute_miss_forest(): MissForest Imputation
impute_ppca(): PPCA Imputation
impute_sample_min(): Sample Minimum Imputation
impute_svd(): SVD Imputation
impute_sw_knn(): Sample-wise KNN Imputation
impute_zero(): Zero Imputation

Filtering

remove_constant(): Remove Constant Variables
remove_low_cv(): Remove Variables with Low Coefficient of Variation
remove_low_expr(): Remove Variables with Low Expression
remove_low_var(): Remove Variables with Low Variance Remove Variables with Low Variance
remove_rare(): Remove Rare Variables with Too Many Missing Values

Batch Effects

correct_batch_effect(): Correct Batch Effect
detect_batch_effect(): Detect batch effect
plot_batch_pca(): Plot PCA Score by Batch

Protein Adjustment

adjust_protein(): Adjust Protein Expression

Annotation

add_site_seq(): Add site-specific sequence information.

QC Plots

plot_cv_dent(): Plot CV Density
plot_int_boxplot(): Plot Log-Intensity Boxplots by Sample
plot_missing_bar(): Plot Missing Value Proportions by Sample or Variable
plot_missing_heatmap(): Plot Missing Value Heatmap
plot_rep_scatter(): Plot Replicate Scatter Plots
plot_rle(): Plot Relative Log Expression (RLE) Boxplots
plot_tic_bar(): Plot Total Intensity by Sample
plot_rank_abundance(): Plot Rank Abundance