The input data required for greatR is a data frame that
contains gene expression time-course data with all replicates. The
illustrated diagram below shows the required structure of the
input.
This data frame must contain reference and query expression data which users wish to compare, and the following five columns:
-
gene_id: locus name or unique ID of each gene. -
accession: accession or name of the reference and query data to compare. -
timepoint: time points of the gene expression data. -
expression_value: desired expression values or measure of the abundance of gene or transcripts which users wish to compare. This value can be RPM, RPKM, FPKM, TPM, TMM, DESeq, SCnorm, GeTMM, ComBat-Seq, and raw reads counts. -
replicate: biological replicate ID for an expression value at a particular time point.
Below we can see a real example of how the input data
should look like:
| gene_id | accession | timepoint | expression_value | replicate |
|---|---|---|---|---|
| BRAA02G018970.3C | Ro18 | 11 | 0.3968734 | Ro18-11-a |
| BRAA02G018970.3C | Ro18 | 11 | 1.4147711 | Ro18-11-b |
| BRAA02G018970.3C | Col0 | 7 | 0.4667855 | Col0-07-a |
| BRAA02G018970.3C | Col0 | 7 | 0.0741901 | Col0-07-b |