TROM (version 1.0)

ws.trom.orthologs: Within-species transcriptome mapping using ortholog genes

Description

This function calculates the TROM scores in comparing samples from the same species. TROM score = -log$_{10}$(Bonferroni-corrected p-value from a hypergeometric test), with a minimum value of 0. And the hypergeometric test is performed on the genes having orthologs in the other species.

Usage

ws.trom.orthologs(sp1_sp2_orthologs, sp_gene_expr, z_thre = 1.5, 
                  FPKM_thre =1, i, provide = FALSE, gene_lists, 
                  save_overlap_genes = FALSE)

Arguments

sp1_sp2_orthologs

a data frame containing ortholog gene pairs between species 1 and 2.

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.

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.

i

an integer specifying which column of sp1_sp2_orthologs the species corresponds to. 1 for the first column and 2 for the second column.

provide

a Boolean value indicating whether associated geness 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 a .xlsx file. If save_overlap_genes = TRUE, this function outputs the overlap genes (within ortholog genes) to "within-speci

Value

• A matrix of within-species TROM scores using ortholog genes, 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 orthologs 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. This function outputs the within-species TROM scores into an .xlsx file named "within-species TROM scores (with ortholog genes).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

ws.trom, bs.trom.

Examples

## Calculating transcriptome overlap measure within D. melanogaster
## using ortholog genes

## without user-provided gene lists
## The .rda files used in this example can be downloaded and unzipped from
## http://www.stat.ucla.edu/~jingyi.li/packages/TROM/TROM_Rdata.zip.
load("dm_gene_expr.rda")
load("dm_ce_orthologs.rda")
dm_trom_orth <- ws.trom.orthologs(sp1_sp2_orthologs = dm_ce_orthologs, 
                   sp_gene_expr = dm_gene_expr, 
                   z_thre = 1.5, FPKM_thre = 1, 
                   i = 1, provide = FALSE, save_overlap_genes = FALSE)


## with user-provided gene lists
gene_lists <- system.file("dm_associated_orthologs.xlsx", package = "TROM")
dm_trom_orth2 <- ws.trom.orthologs(sp1_sp2_orthologs = dm_ce_orthologs, 
                   i = 1, provide = TRUE, gene_lists = gene_lists,
                   save_overlap_genes = FALSE)