# Single Cell Feature Identification with Network Topology

## Documentation for package ‘SiFINeT’ version 1.13

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

assign_shared_feature | assign_shared_feature
cal_coexp | cal_coexp This function calculates the coexpression patterns between genes and returns the coexpression matrix.
cal_coexp_sp | cal_coexp_sp This function calculates the coexpression patterns between genes in sparse matrix and returns the coexpression matrix.
cal_conn | cal_conn This function calculates the first 3 order connectivities for each gene and returns the list of vectors of connectivities.
cal_connectivity | cal_connectivity
create_network | create_network
create_SiFINeT_object | create_SiFINeT_object
enrich_feature_set | enrich_feature_set
EstNull | EstNull This function is a Rcpp version of Wenguang Sun and Tony T. Cai's EstNull.func R function, estimating null distribution from data. Sun, W., & Cai, T. T. (2007). Oracle and Adaptive Compound Decision Rules for False Discovery Rate Control. Journal of the American Statistical Association, 102(479), 901–912.
extract_subnetwork | extract_subnetwork
feature_coexp | feature_coexp
filter_lowexp | filter_lowexp
find_unique_feature | find_unique_feature
geneset_topology | geneset_topology
norm_FDR_SQAUC | norm_FDR_SQAUC The function controls the false discovery rate (FDR) of coexpression patterns using SQAUC method Jichun Xie and Ruosha Li. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates". In: J R Stat Soc Series B Stat Methodol (2018). doi: 10.1111/rssb.12288.
quantile_thres | quantile_thres
SiFINeT | The SiFINeT Class
SiFINeT-class | The SiFINeT Class