trim_net: trim_net trimms the weighted neighborhood network by removing...

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

trim_net trimms the weighted neighborhood network by removing edges of lower weights

Usage

trim_net(nb12, textSize = 20, baseName = NULL, method = "mst",
  start = "MDP_6", writeRes = TRUE)

Arguments

nb12	a matrix of weighted neighborhood network, column and row names are landmarks, the values represent the weights of the edges connecting two landmarks
textSize	the size of text
baseName	a character string indicating the prefix name of resulting files
method	trimming method, method can be one of "TrimNet" or "mst". When method="TrimNet" the initial node needs to be specified. Default is "mst"
start	starting landmark, needs to be specified when method="TrimNet".
writeRes	a boolean to indicate whether to save result files

Value

a matrix of trimmed state transition network, column and row names are landmarks, the values are 0 or 1 indicating whether the two landmarks are connected.

Examples

## Not run: 
baseName = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG";
trimmed_net <- trim_net(neighbor_network,textSize=30,
                        baseName = baseName,
                        method = "mst")

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.