[R] remove quotes from matrix

Tue Sep 19 17:38:13 CEST 2017

Your description was confusing. You do not have row names that are non-numeric:

> str(dta)
'data.frame':   5 obs. of  5 variables:
 $ Sub_Pathways: Factor w/ 79 levels "Acetylated_Peptides",..: 3 3 3 3 3
 $ BMI_beta    : num  0.2382 -0.313 0.1238 0.3035 -0.00982
 $ SAT_beta    : num  -0.0241 -1.9751 0.4095 0.4861 0.3293
 $ VAT_beta    : num  0.942 -2.22 0.68 0.708 0.016
 $ VSR_beta    : num  0.2469 -0.2354 0.0554 0.0134 -0.0435

You have a column that is a factor with 79 levels. That cannot be row names because you indicated that the original data was 734*22 dimensions and row names cannot have duplications. If you want numeric values, you need to strip off the first column:

> as.matrix(dta[ , -1])
  BMI_beta SAT_beta VAT_beta VSR_beta
1  0.23820 -0.02409  0.94180  0.24690
2 -0.31300 -1.97510 -2.22040 -0.23540
3  0.12380  0.40950  0.68050  0.05539
4  0.30350  0.48610  0.70830  0.01337
5 -0.00982  0.32930  0.01597 -0.04353

If you just want to print the character values without quotes:

> print(as.matrix(dta), quote=FALSE)
  Sub_Pathways          BMI_beta SAT_beta VAT_beta VSR_beta
1 Alanine_and_Aspartate  0.23820 -0.02409  0.94180  0.24690
2 Alanine_and_Aspartate -0.31300 -1.97510 -2.22040 -0.23540
3 Alanine_and_Aspartate  0.12380  0.40950  0.68050  0.05539
4 Alanine_and_Aspartate  0.30350  0.48610  0.70830  0.01337
5 Alanine_and_Aspartate -0.00982  0.32930  0.01597 -0.04353

But do not forget that they are still character strings.

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg holly
Sent: Tuesday, September 19, 2017 10:21 AM
To: Duncan Murdoch <murdoch.duncan at gmail.com>
Cc: r-help mailing list <r-help at r-project.org>
Subject: Re: [R] remove quotes from matrix

Dear all;

Thanks. Here are the dput results as Duncan suggested.

Regards,

Greg

structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label = c("Acetylated_Peptides", "Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar", "Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine", "Diacylglycerol", "Dipeptide", "Dipeptide_Derivative", "Disaccharides_and_Oligosaccharides",
"Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)", "Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched", "Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy", "Fatty_Acid,_Monohydroxy", "Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)", "Fatty_Acid_(also_BCAA)", "Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide", "Fructose,_Mannose_and_Galactose",
"Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid", "Glycine,_Serine_and_Threonine", "Glycogen", "Glycolysis,_Gluconeogenesis,_and_Pyruvate",
"Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine", "Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine", "Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid", "Lysoplasmalogen", "Medium_Chain_Fatty_Acid", "Methionine,_Cysteine,_SAM_and_Taurine",
"Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide", "Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose", "Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen", "Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
"Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
"Purine,_Adenine_containing", "Purine,_Guanine_containing", "Pyrimidine,_Cytidine_containing",
"Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing", "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid", "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol", "TCA_Cycle", "Tocopherol", "Tryptophan", "Urea_cycle;_Arginine_and_Proline",
"Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382, -0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751, 0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805, 0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337, -0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta", "VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")

On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

> On 19/09/2017 9:47 AM, greg holly wrote:
>
>> Hi all;
>>
>> I have data at 734*22 dimensions with rows and columns names are 
>> non-numeric.When I convert this data into matrix then all values show 
>> up with quotes. Then when I use x1= noquotes(x) to remove the quotes 
>> from the matrix then non-numeric row names remain all other values in 
>> matrix disappear.
>>
>> Your help is greatly appreciated.
>>
>>
>
> Matrices in R can have only one type.  If you start with a dataframe 
> and any columns contain character data, all entries will be converted 
> to character, and the matrix will be displayed with quotes.
>
> When you say all values disappear, it sounds as though you are 
> displaying strings containing nothing (or just blanks).  Those will be displayed as ""
> normally, but if the matrix is marked to display without quotes, they 
> are displayed as empty strings, so it will appear that nothing is displayed.
>
> You can see the structure of the original data using the str() 
> function, e.g. str(x) should display types for each column.
>
> If this isn't enough to explain what's going on, please show us more 
> detail.  For example, show us the result of
>
> y <- x[1:5, 1:5]
> dput(y)
>
> both before and after converting x to a matrix.
>
> Duncan Murdoch
>

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