Package index • glyexp

Experiment Creation and Conversion

experiment() is_experiment(): Create a new experiment

as_se(): Convert experiment to SummarizedExperiment

from_se(): Convert SummarizedExperiment to experiment

as_tibble(<glyexp_experiment>): Convert an experiment to a tibble

Experiment Inspection

experiment() is_experiment(): Create a new experiment

get_expr_mat(): Get the expression matrix of an experiment

get_sample_info(): Get the sample information of an experiment

get_var_info(): Get the variable information of an experiment

get_meta_data() get_exp_type() get_glycan_type(): Get the meta data of an experiment

count_compositions() count_structures() count_peptides() count_glycopeptides() count_glycoforms() count_proteins() count_glycosites(): Identification overview

dim(<glyexp_experiment>) `dim<-`(<glyexp_experiment>): Dimensions of an experiment

dimnames(<glyexp_experiment>): Dimname for experiment

n_samples() n_variables(): Get number of samples or variables of an experiment

samples() variables(): Get Samples or Variables of an Experiment

Dplyr-Style Manipulation

arrange_obs() arrange_var(): Arrange sample or variable information

filter_obs() filter_var(): Filter samples or variables of an experiment

left_join_obs() inner_join_obs() semi_join_obs() anti_join_obs() left_join_var() inner_join_var() semi_join_var() anti_join_var(): Join data to sample or variable information

mutate_obs() mutate_var(): Mutate sample or variable information

rename_obs() rename_var(): Rename columns in the sample or variable information tibble

select_obs() select_var(): Select columns of the sample or variable information tibble

slice_obs() slice_var() slice_head_obs() slice_head_var() slice_tail_obs() slice_tail_var() slice_sample_obs() slice_sample_var() slice_max_obs() slice_max_var() slice_min_obs() slice_min_var(): Slice sample or variable information

Base-Style Manipulation

merge(<glyexp_experiment>): Merge two experiments

split(<glyexp_experiment>): Split an experiment

`[`(<glyexp_experiment>) `[<-`(<glyexp_experiment>): Subsetting experiments

Other Functions

set_meta_data() set_exp_type() set_glycan_type(): Set the meta data of an experiment

Datasets

toy_experiment: Toy experiment

real_experiment: Real glycoproteomics experiment

real_experiment2: Real glycomics experiment