select.associated.genes: Select the associated genes for biological samples of a species

Description

select.associated.genes() finds the ids of associated genes of a species based on criterion: Z-scores \(\ge\) z_thre and saves the results to an .xlsx file.

Usage

select.associated.genes(sp_gene_expr, z_thre = 1.5, 
                        save = TRUE, plot_distribution = 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.

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. This can be specified by users or calculated using choose.z().

save

a Boolean value specifying whether to save the associated genes to an Excel file. If save = TRUE, this function saves the results to an Excel file named "associated genes.xlsx".

plot_distribution

a Boolean value specifying whether to output the distribution of the number of associated genes across different samples. If plot_distribution = TRUE, this function outputs a barplot of the number of associated genes for each sample in a pdf file named "number of sample associated genes.pdf".

Value

a data frame containing the associated genes of every sample from the species. Every column in the data frame stores the associated gene IDs for the corresponding sample.

References

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

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.

Examples

Run this code

# NOT RUN {
## Find the associaed genes 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")
dm_associated_genes <- select.associated.genes(sp_gene_expr = dm_gene_expr, 
                       z_thre = 1.5, save = TRUE, 
                       plot_distribution = TRUE)           
# }