PFP-class: 'PFP-class'

In aib-group/PFP: Pathway Fingerprint Framework in R

Description

An S4 object for storing pathway fingerprint scores information.

Slots

pathways_score,

a list contains PFP_score, stats_test, genes_score. PFP_score is a numeric score indicating the performance of a gene_list in some pathways.stats_test is a statistic test for the PFP_score. genes_score is the detail scores of every gene in the gene_list.

refnet_info,

a data.frame, which contains the specific information of pathway networks. Just be the same as net_info in PFPRefnet-class, including the index, id, name, group and species.

method

• pathways_score, signature(object = "PFP"): extract the pathways score

• refnet_info, signature(object = "PFP"): extract the pathway networks information

• PFP_score, signature(object = "PFP"): extract the PFP score

• stats_test, signature(object = "PFP"): extract p_value & p_adj_value

• genes_score, signature(object = "PFP", index=NULL, index_type = c("pathway_id","pathway_name","slice")): extract the genes score

• refnet_names, signature(object = "PFP"): extract the refnet names

• sub_PFP, signature(object = "PFP", group_name = NULL, index = NULL, index_type = c("slice","pathway_id","pathway_name")) subset of PFP object

• show_PFP, signature(object = "PFP"): display methods for S4 classes PFP

• plot_PFP, signature(object, type = "character", p_size = "numeric", l_size = 'numeric'): plot the Pathway Fingerprint.

• rank_PFP signature(object = "PFP", total_rank = FALSE, decreasing=TRUE) sort the PFP score.

See Also

pathways_score-methods, refnet_info-methods,PFP_score-methods, stats_test-methods, genes_score-methods, refnet_names-methods, sub_PFP-methods, show_PFP-methods, plot_PFP-methods, rank_PFP-methods,

Examples

data(PFP_test1)
PFP_test1

aib-group/PFP documentation built on Dec. 27, 2020, 1:13 a.m.