| Title: | Cleans Spectrophotometry Data Obtained from the Denovix DS-11 Instrument |
| Version: | 2.1.0 |
| Description: | Cleans spectrophotometry data obtained from the Denovix instrument. The package also provides an option to normalize the data in order to compare the quality of the samples obtained. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Suggests: | knitr, learnr, rmarkdown, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Imports: | data.table, janitor, readxl, tibble, dplyr, tidyr, stats, utils |
| Depends: | R (≥ 2.10) |
| LazyData: | true |
| URL: | https://github.com/AlphaPrime7/tidyDenovix |
| BugReports: | https://github.com/AlphaPrime7/tidyDenovix/issues |
| NeedsCompilation: | no |
| Packaged: | 2024-01-12 03:22:36 UTC; GrandProf |
| Author: | Tingwei Adeck 
[aut, cre] |
| Maintainer: | Tingwei Adeck <awesome.tingwei@outlook.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-01-18 10:00:02 UTC |
tidyDenovix: Cleans Spectrophotometry Data Obtained from the Denovix DS-11 Instrument
Description
Cleans spectrophotometry data obtained from the Denovix instrument. The package also provides an option to normalize the data in order to compare the quality of the samples obtained.
Author(s)
Maintainer: Tingwei Adeck awesome.tingwei@outlook.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/AlphaPrime7/tidyDenovix/issues
Title: Enum function
Description
Title: Enum function
Usage
REnum(elist)
Arguments
elist |
A list with variable binding. |
Value
The list supplied by the user.
Author(s)
Tingwei Adeck
Examples
cols = list('x260' = 1, 'x280' = 2, 'x230' = 3)
qc = REnum(cols)
a = (qc$x260)
Title: Extract key colnames from the Denovix data frame
Description
Title: Extract key colnames from the Denovix data frame
Usage
extract_col_names(xdf)
Arguments
xdf |
The data frame for colname(s) extraction. |
Value
A vector of key column names.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
col_names = extract_col_names(rna_data)
Title: Extract sample names from the Denovix data frame
Description
Title: Extract sample names from the Denovix data frame
Usage
extract_sample_names(dfile, file_type = NULL)
Arguments
dfile |
The denovix raw file for sample name(s) extraction. |
file_type |
The type of file. |
Value
A vector of sample names.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
esn = extract_sample_names(fpath, file_type = 'csv')
Title: Extract wavelength
Description
Title: Extract wavelength
Usage
extract_wavelength(xdf)
Arguments
xdf |
The original data frame derived from importing Denovix data. |
Value
A numeric data frame for the wavelength attribute.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
wl = extract_wavelength(rna_data)
Title: File Extension Finder
Description
Title: File Extension Finder
Usage
file_ext(epath)
Arguments
epath |
File path. |
Value
A string representing the file extension.
Author(s)
Unknown (Adapted by Tingwei Adeck)
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
ext = file_ext(fpath)
Title: Wavelength quality control
Description
Title: Wavelength quality control
Usage
lambda_check(
qdf,
sample_type = c("RNA", "DNA"),
check_level = c("strict", "lax")
)
Arguments
qdf |
A data frame with quality attributes. |
sample_type |
The type of sample under investigation. |
check_level |
The level of strictness based on sample type. |
Value
A data frame that meets the quality check criteria.
Note
Some key assumptions are made about quality for RNA or DNA. At the moment column names is the main issue found with using this approach.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
qc_check = lambda_check(rna_data,sample_type='RNA',check_level='lax')
Title: Wavelength quality control
Description
Title: Wavelength quality control
Usage
lambda_check_source(
odf,
sample_type = c("RNA", "DNA"),
check_level = c("strict", "lax")
)
Arguments
odf |
A data frame with quality attributes. |
sample_type |
The type of sample under investigation. |
check_level |
The level of strictness based on sample type. |
Value
A vector of sample names for the different QC criteria.
Note
Some key assumptions are made about quality for RNA or DNA. At the moment column names is the main issue found with using this approach.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
qc_check = lambda_check_source(rna_data,sample_type='RNA',check_level='lax')
Title: Make wavelength
Description
Title: Make wavelength
Usage
make_wavelength()
Value
A numeric data frame for the wavelength attribute.
Author(s)
Tingwei Adeck
Examples
wl = make_wavelength()
Title: Min-Max normalization of attributes that require normalization
Description
Title: Min-Max normalization of attributes that require normalization
Usage
min_max_norm(x)
Arguments
x |
A single value from an attribute passed in the function for normalization. |
Value
A normalized value (value between 1 and 0)
Note
lapply is needed to apply the function across several columns in a data set.
Author(s)
Tingwei Adeck (Adapted from Statology)
References
https://www.statology.org/how-to-normalize-data-in-r/
Examples
test_df <- as.data.frame(c(seq(40)))
colnames(test_df) <- "test"
test_df_norm <- lapply(test_df[1:ncol(test_df)], min_max_norm)
Title: Quality Control data frame
Description
Title: Quality Control data frame
Usage
qc_attributes(dfile, file_type = NULL, xdf)
Arguments
dfile |
The Denovix file path. |
file_type |
The type of file. |
xdf |
The Denovix data frame. |
Value
A quality control data frame.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
qc_attributes = qc_attributes(fpath, file_type = 'csv', rna_data)
Title: Read Denovix files
Description
A function read Denovix data files.
Usage
read_denovix(dfile)
Arguments
dfile |
A Denovix file or path to the Denovix file. |
Value
A data frame.
Note
Denovix files can be saved as csv, txt or even excel files. This function accounts for these file types.
Author(s)
Tingwei Adeck
See Also
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix(fpath)
Title: Read Denovix files
Description
A function read Denovix data files.
Usage
read_denovix_data(dfile, file_type = c("csv", "txt", "excel"))
Arguments
dfile |
A Denovix file or path to the Denovix file. |
file_type |
The file type being imported. |
Value
A data frame.
Note
Denovix files can be saved as csv, txt or even excel files. This function accounts for these file types.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = read_denovix_data(fpath, file_type = 'csv')
rna1.
Description
An excel file version of the Denovix Spectrophotometry data.
Usage
rna1
Format
An object of class tbl_df (inherits from tbl, data.frame) with 14 rows and 151 columns.
rna2.
Description
A csv file version of the Denovix Spectrophotometry data.
Usage
rna2
Format
An object of class data.frame with 15 rows and 151 columns.
rna3.
Description
A csv file version of the Denovix Spectrophotometry data.
Usage
rna3
Format
An object of class data.frame with 15 rows and 152 columns.
spec.
Description
A txt file version of the Denovix Spectrophotometry data.
Usage
spec
Format
An object of class data.frame with 15 rows and 151 columns.
Title: Clean data from the Denovix DS-11 instrument
Description
Title: Clean data from the Denovix DS-11 instrument
Usage
tidyDenovix(
dfile,
file_type = NULL,
sample_type = c("RNA", "DNA"),
check_level = c("strict", "lax"),
qc_omit = NULL,
normalized = c("yes", "no"),
fun = NA
)
Arguments
dfile |
The raw file obtained from the machine. |
file_type |
The file type specification. |
sample_type |
The sample type specification used in quality control. |
check_level |
The level of quality control performed. |
qc_omit |
Takes 'yes' or 'no' and determines if the qc data would be provided. |
normalized |
Takes 'yes' or 'no'. |
fun |
A parameter used for boolean expressions. |
Value
A cleaned data frame with attribute names in some instances.
Note
The strict level of QC yields a data frame with no attribute names. This will be worked on so that users get the sample names for their data.
Author(s)
Tingwei Adeck
Examples
fpath <- system.file("extdata", "rnaspec2018.csv", package = "tidyDenovix", mustWork = TRUE)
rna_data = tidyDenovix(fpath, file_type = 'csv', sample_type = 'RNA', check_level = 'lax')