TROM (version 1.0)

ws.trom: Within-species transcriptome mapping

Description

This function calculates the TROM scores in comparing/mapping samples from the same species. TROM score = -log$_{10}$(Bonferroni-corrected p-value from a hypergeometric test), with a minimum value of 0.

Usage

ws.trom(sp_gene_expr, z_thre = 1.5, FPKM_thre = 1, 
    provide = FALSE, gene_lists = "", save_overlap_genes = 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.

z_thre

a numeric value specifiying the Z-score threshold used to select associated genes, whose Z-scores $\ge$ z_thre. Defaults to 1.5.

FPKM_thre

a numeric value specifying FPKM threshold used to select associated genes, whose FPKM $\ge$ FPKM_thre. Defaults to 1.

provide

a Boolean value indicating whether associated genes are user-provided. If provide = TRUE, the users need to provide lists of genes that they think can represent the transcriptome characteristics of different samples.

gene_lists

an .xlsx file containing user-provided gene lists. It is required when provide = TRUE.

save_overlap_genes

a Boolean value indicating whether the users want to save overlap genes between every two samples from the species to an .xlsx file. If save_overlap_genes = TRUE, this function outputs the overlap genes to "within-species overlapping genes be

Value

• A square matrix of within-species TROM scores, where rows and columns correspond to the samples of the species respectively.

Details

If provide = TRUE, users provide gene lists with gene_lists to calculate the TROM scores; otherwise, the function will automatically select associated genes based on the criterion: Z-scores $\ge$ z_thre and FPKM $\ge$ FPKM_thre. If provided, gene_lists should be a one-sheet Excel file. In the Excel file, rows represent gene ids and columns represent biological samples. Each column of the file stores the user-provided genes corresponding to the sample of that column. Please note that different columns may have different numbers of rows. This function outputs the within-species TROM scores into an .xlsx file named "within-species TROM scores.xlsx".

References

Li JJ, Huang H, Bickel PJ, & Brenner SE (2014). Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research, 24(7), 1086-1101.

See Also

bs.trom, ws.trom.orthologs

Examples

## Calculating transcriptome overlap measure within D. melanogaster 

## without user-provided gene lists
## dm_gene_expr.rda can be downloaded and unzipped from
## http://www.stat.ucla.edu/~jingyi.li/packages/TROM/TROM_Rdata.zip.
load("dm_gene_expr.rda")
dm_trom <- ws.trom(sp_gene_expr = dm_gene_expr, z_thre = 1.5, 
                     FPKM_thre = 1, provide = FALSE, save_overlap_genes = TRUE)

## with user-provided gene lists
gene_lists <- system.file("dm_associated_genes.xlsx", package = "TROM")
dm_trom_2 <- ws.trom(provide = TRUE, gene_lists = gene_lists)