PFP-class {PFP} | R Documentation

## `PFP-class`

### 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

[Package PFP version 1.2.0 Index]