gravatar for reara

2 hours ago by

Im trying to map my clinical traits file in WGCNA but there seems to be some problem with the mataching (Note- My pheno/trait file has only the fields i require)

Code chunk 7-Read in Clinical Traits csv file

traitData = read.csv("phenofile_reqd_fields.csv");

dim(traitData)
names(traitData)`

dim(traitData)

[1] 2611 11

names(traitData)

[1] "sid" "gender" "race" "ethnic"
[5] "smoking_status" "finalGold" "eosinphl_pct_calc" "monocyt_pct_calc"
[9] "neutrophl_pct_calc" "basophl_pct_calc" "lymphcyt_pct_calc"

-- remove columns that hold information we do not need-my csv file has only the fields i need so im not removing any columns:

allTraits = traitData;
allTraits = allTraits[,];
dim(allTraits)
names(allTraits)

--Form a data frame analogous to expression data that will hold the clinical traits.

femaleSamples = rownames(datExpr0);
traitRows = match(femaleSamples, allTraits$sid);
datTraits = allTraits[traitRows, -1];
rownames(datTraits) = allTraits[traitRows, 1];


dim(allTraits)

[1] 2611 11

names(allTraits)

[1] "sid" "gender" "race" "ethnic"
[5] "smoking_status" "finalGold" "eosinphl_pct_calc" "monocyt_pct_calc"
[9] "neutrophl_pct_calc" "basophl_pct_calc" "lymphcyt_pct_calc"

--Form a data frame analogous to expression data that will hold the clinical traits.

femaleSamples = rownames(datExpr0);
traitRows = match(femaleSamples, allTraits$sid);
datTraits = allTraits[traitRows, -1];
rownames(datTraits) = allTraits[traitRows, 1];

when i run the above i get:

Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':

But ive checked and there are no duplicate records in my data.

Also my allTraits looks like my original csv file with the first column with my "sid" values and has all the values under the column headings.

allTraits

sid gender race ethnic smoking_status finalGold eosinphl_pct_calc monocyt_pct_calc

10010J 2 1 2 1 3 2 7

. 10025W 1 2 2 1 4 0 7

10052Z 1 1 2 2 3 2 9
4 10055F 1 2 2 1 0 3 8
5 10060Y 1 1 2 1 4 3 12
6 10065I 2 1 2 1 1 4 8
7 10076N 1 1 2 1 1 1 7

But my datTraits looks like this-

datTraits

gender race ethnic smoking_status finalGold eosinphl_pct_calc monocyt_pct_calc
NA NA NA NA NA NA NA NA
NA.1 NA NA NA NA NA NA NA
NA.2 NA NA NA NA NA NA NA
NA.3 NA NA NA NA NA NA NA
NA.4 NA NA NA NA NA NA NA
NA.5 NA NA NA NA NA NA NA
NA.6 NA NA NA NA NA NA NA
NA.7 NA NA NA NA NA NA NA

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modified 2 hours ago

written
2 hours ago
by

reara20



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