Question

How to convert relative abundance table to mean ranked abundance table in R

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2.1 years ago

smrutimayipanda ▴ 20

I have a data containing the following:

#mpa_vJan21_CHOCOPhlAnSGB_202103                                                
clade_name  B075Md_output_file  B090Md_output_file  B219Md_output_file  B447Md_output_file  B449Md_output_file  B478Md_output_file  B651Md_output_file  B671Md_output_file  B816Md_output_file  B825Md_output_file      shannon_diversity

    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_SGB1680  12.00431    0   0   0   0.00119 0   0   0.17122 0   0       0.074922491
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_SGB1653  10.22914    0   0   0.00016 0.2956  3.72963 0   0   0   0       0.66943321
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_hominis  9.12261 3.91705 0.01911 0.0003  0   3.39052 0   0   0   0       1.002221034
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_A    6.5243  12.43665    0.11    24.56968    1.98188 2.60397 0   1.34378 0   0       1.35655806
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_A    6.5243  12.43665    0.11    24.56968    1.98188 2.60397 0   1.34378 0   0       1.35655806
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia_timonensis   6.43526 0   0   0   0   1.03691 0   0   0   0       0.40272364
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_C    5.87136 9.08257 1.14649 0.00121 1.59164 2.76605 0   3.42573 0   0       1.567522962
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri_clade_C    5.87136 9.08257 1.14649 0.00121 1.59164 2.76605 0   3.42573 0   0       1.567522962
    k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale  4.80952 6.40274 6.53739 8.20885 11.72238    8.13603 0.38386 7.28658 6.88267 1.77194     2.145222649
    k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens   3.51494 0.21745 0.75646 0   0   3.78288 0   0   0   0       1.03586081
    k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_sp_885   2.2899  0   0   0   1.66894 0.93706 0   0.16017 0   0       1.146359089
    k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter|s__Ruminococcus_torques   1.90517 1.72799 0.71511 1.69515 1.1922  6.69036 13.88819    4.32956 0.64551 5.81669     1.876527875

I want this abundance table to convert into mean ranked abundance table in R specifically. Can anyone please tell me how to do this? I have searched a lot about this but didnt find anything. Thanks!

metagenomics abundance • 805 views

ADD COMMENT • link 2.1 years ago by smrutimayipanda ▴ 20

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That file is giving you the abundance estimates on a per-sample (per-input-bam-file) basis. "Mean abundance" describes mean of those values, i.e., the mean abundance within the cohort.