README.md

In homonecloco/expvip-analysis:

This set of scripts are to analyse the expression on hexaploid wheat (but may be useful for other organisms)

Tables used for plot_genes_report.R

This tables are loaded with the function loadGeneInformation(dir=../TablesForExploration)

$canonicalTranscripts

File : CanonicalTranscript.rds

• Gene
• transcript
• Chr
• Start
• End
• mrna_length
• geneconf If the gene is High Confidence or Low confidence (HC/LC)
• size_cds
• exon_no
• exon_length
• scaled_1per_position
• scaled_5per_position
• X3UTR_length
• X5UTR_length
• intron_length Calculated from mrna_length-exon_length
• chr_group Calculated from 4th character from Chr
• genome Calculated from 5th character from Chr

Only the genes that are present in the $meanTpms table are retained for the reports. The expectation of genes per position is based ONLY on the genes that have geneconf=='HC'

$meanTpms

File: MeanTpms.rds

• value mean TPM
• factor Tissue/stress/age.
• gene
• samples The number of samples used for the average
• subset A name for the analysis where this values where obtained.
• min_mean_tpm The minimum TPM value for at least 1% of the sample used to produce the file.

The file contains the mean TPM per each factor (obtained by replicates) for each gene. When the factor is all_means_filtered the number of samples represent the number of tissues/factors that whent into that category. So when samples == 1 the gene is uniquely expressed.

$triads

File: Triads.rds group_id clust description general_description Central A.dominant B.dominant D.dominant A.suppressed B.suppressed D.suppressed value factor gene samples chr_group triad_sum normalised_triad Distance P.rank min_triad_sums dataset

$triadMovement

File: TriadMovement.rds

• group_id
• factor_count
• central_total_distance
• central_mean_distance
• central_max_distance
• central_sd_distance
• central_max_over_mean
• factor_total_distance
• factor_mean_distance
• factor_max_distance
• factor_sd_distance
• factor_max_over_mean
• category
• sum_mean_tpm
• total_categories
• categories
• Central
• A.dominant
• A.suppressed
• B.dominant
• B.suppressed
• D.dominant
• D.suppressed
• dataset

$gene_universe

File: universe_table.csv

• gene
• dataset

$ontologies

File: OntologiesForGenes.rds

• Gene
• ID
• ontology

$id_names

File: id_names_merged.txt

• V1
• V2

This table gives a human readable version of the ontologies.

Beware, this table doesn't have headers. So when R reads it it automatically assign this names. x§

$WGCNA

File: WGCNA_table.csv Gene ModuleLabels ModuleColors Number_genes_in_module * set

homonecloco/expvip-analysis documentation built on May 22, 2019, 12:42 p.m.