wanjauk / intbt_2020 Goto Github PK

Hi TA,
How do you identify the numeric or the factor data first to replace ''Dog''? Find the following output for perusal:

b = super.fitZig.kv(physeq = phy.temp,factor = "Dog",outDir = outDir,FileName =c("1_25FC_0.2_Dog_GvsB_ASVs"),

•   heatmap.descriptor=c("tax_annot"), main=c("Dog G vs. B, merged taxa"), subt=c("subt = FDR < 0.05,|coeff| >= 1.25, >20%+ in either group"), 
  

•   ordered=TRUE, p=0.05, FC = 1.25, perc=0.2, extra.cols = c("Treatment"))
  

[1] "0 of 10 samples were removed due to missing data"
Default value being used.
Error in super.fitZig.kv(physeq = phy.temp, factor = "Dog", outDir = outDir, :
Dog is a character variable, please convert to numeric or factor data first

Important links:

1. Tutorial site: https://iallali.github.io/DADA2_pipeline/16SrRNA_DADA2_pipeline.html
2. Script used in the tutorial: https://raw.githubusercontent.com/mbbu/intbt_2019/master/Module_5_16S_analysis_pipeline/dada2_pipeline_tutorial.R
3. Required tutorial data: http://web.cbio.uct.ac.za/~gerrit/downloads/dog_stool_full.tgz
4. RefSeq-RDP 16S database: https://zenodo.org/record/3266798/files/RefSeq-RDP16S_v3_May2018.fa.gz

Create an R project called dada2_tutorial_dog and then download the script, tutorial data and database by copying and pasting the following on the linux terminal (on the HPC's RStudio):

• Script
  wget https://raw.githubusercontent.com/mbbu/intbt_2019/master/Module_5_16S_analysis_pipeline/dada2_pipeline_tutorial.R

• Tutorial data
  wget http://web.cbio.uct.ac.za/~gerrit/downloads/dog_stool_full.tgz
  Note: unzip the data using the following: mkdir -p dog_samples && tar -xvzf dog_stool_full.tgz -C dog_samples

• RefSeq-RDP database
  wget https://zenodo.org/record/3266798/files/RefSeq-RDP16S_v3_May2018.fa.gz

Session 1

Important links:

• Module website: https://kviljoen.github.io/H3ABioNet_16S/
• DADA2 nextflow pipeline: https://github.com/grbot/16S-rDNA-dada2-pipeline
• Instructions on running Nextflow DADA2 pipeline: https://github.com/mbbu/Tutorials-software-guide/blob/master/Tutorials/Dada2%20Pipeline/Running%20the%20DADA2%20Nextflow%20pipeline%20on%20test%20data.md
• Nextflow output: https://github.com/wanjauk/intbt_2020/blob/master/Downstream_Analysis_in_R/Session_1_Nextflow_demo/nextflow-demo-out.zip