Comparing assays from two different downloads

microsud_cmd_reprex.R

# installed curatedMetagenomicData from github
suppressPackageStartupMessages({
    library(curatedMetagenomicData)
    library(dplyr)
})

#I download the data in two ways, one select a few CRC studies and the other will multiple studies available.

# specific only crc studies downloaded
suppressMessages({
tse1 <- sampleMetadata |>
    filter(!is.na(age)) |>
    #filter(!is.na(alcohol)) |>
    filter(study_name %in% c("WirbelJ_2018", "VogtmannE_2016", "YuJ_2015", "ZellerG_2014", "YachidaS_2019")) |> 
    filter(body_site == "stool") |>
    select(where(~ !all(is.na(.x)))) |>
    returnSamples("relative_abundance", rownames = "short")
})
tse1

## large data. Multiple studies downloaded at the same time
suppressMessages({
tse2 <- sampleMetadata |>
    filter(!is.na(disease)) |>
    filter(age >=18) |>
    filter(non_westernized == "no") |>
    filter(body_site == "stool") |>
    select(where(~ !all(is.na(.x)))) |>
    returnSamples("relative_abundance", rownames = "short")
})
tse2

# From the downloaded TSEs, tse1 and tse2, select specific study
tse1.sub <- tse1[,colData(tse1)$study_name =="WirbelJ_2018" ]
tse2.sub <- tse2[,colData(tse2)$study_name =="WirbelJ_2018" ]

rowintersect <- intersect(rownames(tse1.sub), rownames(tse2.sub))
colintersect <- intersect(colnames(tse1.sub), colnames(tse2.sub))

# keep same rows and columns
tse1.sub <- tse1.sub[rowintersect, colintersect]
tse2.sub <- tse2.sub[rowintersect, colintersect]


all.equal(assay(tse1.sub, "relative_abundance"), assay(tse2.sub, "relative_abundance"))

# Extract the abundances for Anaerobutyricum hallii first 5 samples. 
data.frame(tse1.sub.A.hallii = assay(tse1.sub, "relative_abundance")["Anaerobutyricum hallii",][1:5],
           tse2.sub.A.hallii = assay(tse2.sub, "relative_abundance")["Anaerobutyricum hallii",][1:5])

devtools::session_info()