microbialgenomics / 2022_rubio_metahiv

Antibiotic Resistance From Shotgun Data - MetaHIV Study

2022_Rubio_MetaHIV

A workflowr project.

2022_rubio_metahiv's Issues

Additional Analysis

• Include RiskGroup2 as covar for analysis at the alpha diversity and beta-diversity
• Search For correlation between CD4 and NadirCD4 and nABR Genes.
• Using NMDS/Bray coordinates explor other covariates with differences in the projected coordinates
• Intracorrelation analysis of ABR Genes. Use Heatmap/dendrogram based on pairwise aBR-correlation. Use complexHeatmap to label genes according to familiy. Question: Does abundance of ABR genes in the same family correlate accross samples? Are there clusters of genes that co-vary together?

Meeting 220831

• - Intracorrelation analysis of ABR Genes. Use Heatmap/dendrogram based on pairwise aBR-correlation. Use complexHeatmap to label genes according to familiy. Question: Does abundance of ABR genes in the same family correlate accross samples? Are there clusters of genes that co-vary together?

• - Contigency table: HIV profile, RiksGroup2 and Microbiome Cluster. Most of MSN are HIV negative? Check

• - Biplot: check envfit function (https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/envfit)

• - Analyse correlations including ratio CD4/CD8

• - Analysis for Profile clinical variable:

• - Join Elite Controller + Viremic

• - Analize each AMR gene independently to look for differences between groups.

• - Divide according to CD4: chech CD4 distribution to decide a cut-off value.

• - Select only MSM group and divide according to CD4. Anayse AMR genes.

• Procrusters analysis comparing Ariba RPKM and Ariba Rarefied

Meeting 200922

• Intracorrelation analysis of ABR Genes. Use Heatmap/dendrogram based on pairwise aBR-correlation. Use complexHeatmap to label genes according to familiy. Question: Does abundance of ABR genes in the same family correlate accross samples? Are there clusters of genes that co-vary together?
• Obtain total number of resistome reads per sample and alayze with clinical variables
• MSM subgroup: analysis according to HIV profile
• AMR significance: plot using ggstatplot
• Resistome: group by AMR Gene Family and Drug Class (Drug Class: subgroup for 23S/16S point muations) (Sum RPKM values)and compare differential groups according to RiskGroup and Microbiome Cluster
• Virulome:
• Curate vfdb_geneannotation.txt and merge with VFSs.xlsx
• Calculate RPKM (using vfdb_setB_geneLengths.txt)
• Perform alpha and beta diversity analysis

Meeting 171122

ECCMID abstract:

• Group HTS+PWID
• Afegir R2 a adonis
• Drug classes/ Gene dfamilies: differentially abundat (2fold change)
• Add figures

Analysis:

• Differentially abundant function: calculate median instead mean
• Add Drug Class colum to Gene family diff table
• Add 2 fold change in table: https://cran.r-project.org/web/packages/rstatix/index.html
• Stratify gene-count by msm/no-msm
• Perform multivariate analysis: endpoint alpha diversity (Gene_ruchness + sexual practice)
• Bipot with grouped data envfit

Paper:

• Revisió bibliografia: resistoma inmunosupressió