choose.z: Choose the suggested threshold of Z-scores
In TROM: Transcriptome Overlap Measure

Description Usage Arguments Details Value Author(s) References See Also Examples

This function calculates the suggested z_thre for within-species comparison. The suggested z_thre gives the most sparse but still stable correspondance map of the transcriptomes.

1	choose.z(sp_gene_expr, mode = FALSE)

`sp_gene_expr`	a data frame containing gene expression estimates of the species; rows correspond to genes; columns (from the second to the last) correspond to samples, with the first column as gene IDs. Required.
`mode`	a Boolean value specifying the method used to select the threshold. If `mode = TRUE`, threshold is selected based on the mode of a density function; otherwise, (mode + sd) is used. Please refer to the reference for more details.

This function calculates the suggested z_thre for the species corresponding to sp_gene_expr to select associated genes and calculate TROM scores. The users can tune z_thre based on the mapping results calculated from the suggested z_thre.

A numeric vector of length one containing the suggested z_thre.

Jingyi Jessica Li, Wei Vivian Li

https://arxiv.org/abs/1601.05158

Li WV, Chen Y and Li JJ (2016). TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples. Statistics in Biosciences. DOI: 10.1007/s12561-016-9163-y

ws.trom, ws.trom.orthologs

## Calculating the suggested z_thre for first 15 stages of D. melanogaster 

## dm_gene_expr.rda can be downloaded and unzipped from
## http://www.stat.ucla.edu/~jingyi.li/packages/TROM/TROM_Rdata.zip
## Not run: 
load("dm_gene_expr.rda")
z_thre1 <- choose.z(dm_gene_expr[, 1:16], mode = FALSE)
z_thre2 <- choose.z(dm_gene_expr[, 1:16], mode = TRUE)

## End(Not run)