TROM (version 1.3)

choose.z: Choose the suggested threshold of Z-scores

Description

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.

Usage

choose.z(sp_gene_expr, mode = FALSE)

Arguments

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.

Value

A numeric vector of length one containing the suggested z_thre.

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.

References

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

See Also

ws.trom, ws.trom.orthologs

Examples

# NOT RUN {
## 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)
# }