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