phyloseq
Handling and analysis of high-throughput microbiome census data

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sample_sums: Returns the total number of individuals observed from each...

sample_sums: Returns the total number of individuals observed from each...
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Usage Arguments Value See Also Examples

View source: R/otuTable-class.R

Description

A convenience function equivalent to rowSums or colSums, but where the orientation of the otu_table is automatically handled.

Usage

1
sample_sums(x)

Arguments

x

otu_table-class, or phyloseq-class.

Value

A named numeric-class length equal to the number of samples in the x, name indicating the sample ID, and value equal to the sum of all individuals observed for each sample in x.

See Also

taxa_sums, rowSums, colSums

Examples

1
2
3
4
data(enterotype)
sample_sums(enterotype)
data(esophagus)
sample_sums(esophagus)

Example output

   AM.AD.1    AM.AD.2  AM.F10.T1  AM.F10.T2    DA.AD.1   DA.AD.1T    DA.AD.2 
 0.9999999  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000 
   DA.AD.3   DA.AD.3T    DA.AD.4    ES.AD.1    ES.AD.2    ES.AD.3    ES.AD.4 
 1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000 
   FR.AD.1    FR.AD.2    FR.AD.3    FR.AD.4    FR.AD.5    FR.AD.6    FR.AD.7 
 1.0000000  1.0000000  0.9999999  1.0000000  1.0000000  1.0000000  1.0000000 
   FR.AD.8    IT.AD.1    IT.AD.2    IT.AD.3    IT.AD.4    IT.AD.5    IT.AD.6 
 1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000001  0.9999999 
   JP.AD.1    JP.AD.2    JP.AD.3    JP.AD.4    JP.AD.5    JP.AD.6    JP.AD.7 
 1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000 
   JP.AD.8    JP.AD.9    JP.IN.1    JP.IN.2    JP.IN.3    JP.IN.4     MH0001 
 1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  0.9999999 
    MH0002     MH0003     MH0004     MH0005     MH0006     MH0007     MH0008 
 0.9999999  1.0000000  1.0000001  0.9999999  1.0000000  1.0000001  1.0000000 
    MH0009     MH0010     MH0011     MH0012     MH0013     MH0014     MH0015 
 0.9999999  1.0000001  1.0000000  1.0000001  1.0000000  1.0000001  1.0000000 
    MH0016     MH0017     MH0018     MH0019     MH0020     MH0021     MH0022 
 0.9999999  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000  0.9999999 
    MH0023     MH0024     MH0025     MH0026     MH0027     MH0028     MH0030 
 0.9999999  1.0000001  1.0000000  1.0000000  1.0000000  1.0000000  1.0000001 
    MH0031     MH0032     MH0033     MH0034     MH0035     MH0036     MH0037 
 0.9999999  1.0000000  1.0000000  1.0000000  0.9999999  1.0000000  1.0000001 
    MH0038     MH0039     MH0040     MH0041     MH0042     MH0043     MH0044 
 1.0000000  0.9999999  1.0000001  1.0000000  1.0000000  1.0000000  1.0000000 
    MH0045     MH0046     MH0047     MH0048     MH0049     MH0050     MH0051 
 0.9999999  0.9999999  1.0000000  1.0000001  1.0000000  1.0000001  0.9999999 
    MH0052     MH0053     MH0054     MH0055     MH0056     MH0057     MH0058 
 1.0000001  1.0000000  1.0000001  1.0000000  1.0000000  1.0000001  0.9999999 
    MH0059     MH0060     MH0061     MH0062     MH0063     MH0064     MH0065 
 0.9999999  0.9999999  1.0000000  1.0000000  0.9999999  1.0000000  1.0000000 
    MH0066     MH0067     MH0068     MH0069     MH0070     MH0071     MH0072 
 1.0000000  1.0000000  1.0000000  1.0000001  1.0000001  0.9999999  1.0000000 
    MH0073     MH0074     MH0075     MH0076     MH0077     MH0078     MH0079 
 1.0000000  0.9999999  1.0000001  1.0000000  1.0000000  0.9999999  1.0000001 
    MH0080     MH0081     MH0082     MH0083     MH0084     MH0085     MH0086 
 0.9999999  1.0000001  1.0000000  1.0000000  1.0000000  0.9999999  1.0000000 
    TS1_V2    TS10_V2   TS100_V2 TS101.2_V2   TS103_V2   TS104_V2   TS105_V2 
 0.9998830  0.9998700  0.9998790  0.9998720  0.9998710  0.9998710  0.9998630 
  TS106_V2   TS107_V2   TS109_V2    TS11_V2   TS110_V2   TS111_V2   TS115_V2 
 0.9998710  0.9998781  0.9998710  0.9998690  0.9998710  0.9998880  0.9998810 
  TS116_V2   TS117_V2   TS118_V2   TS119_V2    TS12_V2   TS120_V2   TS124_V2 
 0.9998920  0.9998680  0.9998680  0.9998750  0.9998620  0.9998560  0.9998750 
  TS125_V2   TS126_V2   TS127_V2   TS128_V2   TS129_V2    TS13_V2   TS130_V2 
 0.9998790  0.9998830  0.9998800  0.9998770  0.9998740  0.9998850  0.9998590 
  TS131_V2   TS132_V2   TS133_V2   TS134_V2   TS135_V2   TS136_V2   TS137_V2 
 0.9998690  0.9998660  0.9998720  0.9998680  0.9998710  0.9998770  0.9998740 
  TS138_V2   TS139_V2    TS14_V2   TS140_V2   TS141_V2   TS142_V2   TS143_V2 
 0.9998700  0.9998750  0.9998940  0.9998710  0.9998750  0.9998800  0.9998880 
  TS144_V2   TS145_V2   TS146_V2   TS147_V2   TS148_V2   TS149_V2    TS15_V2 
 0.9998790  0.9998650  0.9998760  0.9998700  0.9998860  0.9998901  0.9998930 
  TS150_V2   TS151_V2   TS152_V2   TS153_V2 TS154.2_V2   TS155_V2   TS156_V2 
 0.9998771  0.9998800  0.9998680  0.9998730  0.9998660  0.9998700  0.9998730 
   TS16_V2   TS160_V2   TS161_V2   TS162_V2   TS163_V2   TS164_V2   TS165_V2 
 0.9998750  0.9998740  0.9998600  0.9998620  0.9998660  0.9998730  0.9998809 
  TS166_V2   TS167_V2   TS168_V2   TS169_V2    TS17_V2   TS170_V2   TS178_V2 
 0.9998760  0.9998830  0.9998730  0.9998800  0.9998620  0.9998640  0.9998720 
  TS179_V2   TS180_V2   TS181_V2   TS182_V2   TS183_V2   TS184_V2   TS185_V2 
 0.9998740  0.9998650  0.9998741  0.9998820  0.9998720  0.9998630  0.9998690 
  TS186_V2    TS19_V2   TS190_V2   TS191_V2   TS192_V2   TS193_V2   TS194_V2 
 0.9998650  0.9998881  0.9998721  0.9998660  0.9998700  0.9998650  0.9998700 
  TS195_V2     TS2_V2    TS20_V2    TS21_V2    TS22_V2    TS23_V2    TS25_V2 
 0.9998690  0.9998960  0.9998940  0.9998920  0.9998811  0.9998650  0.9998800 
   TS26_V2    TS27_V2    TS28_V2    TS29_V2     TS3_V2    TS30_V2    TS31_V2 
 0.9998880  0.9998980  0.9998810  0.9998701  0.9998800  0.9998710  0.9998840 
   TS32_V2    TS33_V2    TS34_V2    TS35_V2    TS37_V2    TS38_V2    TS39_V2 
 0.9998810  0.9998880  0.9998700  0.9998820  0.9998720  0.9998740  0.9998790 
    TS4_V2    TS43_V2    TS44_V2    TS49_V2     TS5_V2    TS50_V2    TS51_V2 
 0.9998690  0.9998810  0.9998690  0.9998860  0.9998820  0.9998730  0.9999070 
   TS55_V2    TS56_V2    TS57_V2     TS6_V2    TS61_V2    TS62_V2    TS63_V2 
 0.9998700  0.9998710  0.9998640  0.9998860  0.9998650  0.9998670  0.9998710 
   TS64_V2    TS65_V2    TS66_V2    TS67_V2    TS68_V2    TS69_V2     TS7_V2 
 0.9998800  0.9998760  0.9998750  0.9998630  0.9998740  0.9998741  0.9998860 
   TS70_V2    TS71_V2    TS72_V2    TS73_V2    TS74_V2    TS75_V2    TS76_V2 
 0.9998770  0.9998780  0.9998720  0.9998740  0.9998790  0.9998590  0.9998740 
   TS77_V2    TS78_V2     TS8_V2    TS82_V2    TS83_V2    TS84_V2    TS85_V2 
 0.9998721  0.9998670  0.9998931  0.9998660  0.9998630  0.9998720  0.9998650 
   TS86_V2    TS87_V2    TS88_V2    TS89_V2     TS9_V2    TS90_V2    TS91_V2 
 0.9998771  0.9998830  0.9998630  0.9998700  0.9998800  0.9998810  0.9998621 
   TS92_V2    TS94_V2    TS95_V2    TS96_V2    TS97_V2    TS98_V2  TS99.2_V2 
 0.9998650  0.9998720  0.9998750  0.9998780  0.9998720  0.9998640  0.9998640 
  B   C   D 
203 255 219 
Warning message:
system call failed: Cannot allocate memory

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.

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Package overview README.md Basic storage, access, and manipulation of phylogenetic sequencing data with *phyloseq* Example using Negative Binomial in Microbiome Differential Abundance Testing phyloseq Frequently Asked Questions (FAQ) Vignette for phyloseq: Analysis of high-throughput microbiome census data

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