Data science

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Python

R

Python vs R

R, Python & Julia in data science : A comparison

Datacamp

Machine Learning

How to prepare data for collaboration

How to share data for collaboration. Especially Page 7 has some (raw data) variable coding guidelines.

  • naming variables: using meaning variable names, no spacing in column header, avoiding separator (except an underscore)
  • coding variables: be consistent, no spelling error
  • date and time: YYYY-MM-DD (ISO 8601 standard). A gene symbol "Oct-4" will be interpreted as a date and reformatted in Excel.
  • missing data: "NA". Not leave any cells blank.
  • using a code book file (*.docx for example): any lengthy explanation about variables should be put here. See p5 for an example.

Five types of data:

  • continuous
  • oridinal
  • categorical
  • missing
  • censored

Some extra from Data organization in spreadsheets (the paper appears in American Statistician)

  • No empty cells
  • Put one thing in a cell
  • Make a rectangle
  • No calculation in the raw data files
  • Create a data dictionary (same as code book)

Data Organization in Spreadsheets

Data Organization in Spreadsheets Broman & Woo 2018

Gene name errors from Excel

length(x)
# [1] 28109
length(grep("march", x, ignore.case=T))
# [1] 11
length(grep("sep", x, ignore.case=T))
# [1] 24
length(grep("oct", x, ignore.case=T))
# [1] 0
length(grep("dec", x, ignore.case=T))
# [1] 6
grep("sep", x, ignore.case=T, value=T)
 [1] "RNaseP_nuc"             "SEP15"                  "SEPHS1"
 [4] "SEPHS2"                 "SEPN1"                  "SEPP1"
 [7] "SEPSECS"                "SEPT1"                  "SEPT10"
[10] "SEPT11"                 "SEPT12"                 "SEPT14"
[13] "SEPT2"                  "SEPT3"                  "SEPT4"
[16] "SEPT5-GP1BB"            "SEPT6"                  "SEPT7"
[19] "SEPT7P2"                "SEPT7P9"                "SEPT8"
[22] "SEPT9"                  "SEPW1"                  "septin 9/TNRC6C fusion"

# Count non-alphanumeric symbols from a string
ind <- grep("[^[:alnum:] ]", x)
length(ind)
# [1] 1108

# Some cases: 
# "5S_rRNA"
# "HGC6.1.1"
# "Ig alpha 1-[alpha]2m"
# "T-cell receptor alpha chain variable ..."
# "TRA@"
# "TRNA_Ala"
# "TTN-AS1"
# "aromatase cytochrome P-450 (P-450AROM)"
# "immunoglobulin epsilon chain constant..."
# "septin 9/TNRC6C fusion"

A real example: 

> data.frame(GENEID[i, 1], pull(xcsv, 1)[i], row.names = NULL)
   GENEID.i..1. pull.xcsv..1..i.
1         1-Dec             DEC1
2         1-Mar            MARC1
3         2-Mar            MARC2
4         1-Mar           MARCH1
5        10-Mar          MARCH10
6        11-Mar          MARCH11
7         2-Mar           MARCH2
8         3-Mar           MARCH3
9         4-Mar           MARCH4
10        5-Mar           MARCH5
11        6-Mar           MARCH6
12        7-Mar           MARCH7
13        8-Mar           MARCH8
14        9-Mar           MARCH9
15       15-Sep            SEP15
16        1-Sep            SEPT1
17       10-Sep           SEPT10
18       11-Sep           SEPT11
19       12-Sep           SEPT12
20       14-Sep           SEPT14
21        2-Sep            SEPT2
22        3-Sep            SEPT3
23        4-Sep            SEPT4
24        6-Sep            SEPT6
25        7-Sep            SEPT7
26        8-Sep            SEPT8
27        9-Sep            SEPT9

Also it is possible the gene names start with a numeric number. 

> grep("^[0-9]", pull(xcsv, 1), value = TRUE)
[1] "5S_rRNA"   "5_8S_rRNA" "6M1-18"    "7M1-2"     "7SK"

Check using the R package 

> library(HGNChelper)
> GENEID[grep("^[0-9]", GENEID[,1]), 1] |> checkGeneSymbols()
Maps last updated on: Thu Oct 24 12:31:05 2019
           x Approved    Suggested.Symbol
1    5S_rRNA    FALSE                <NA>
2  5_8S_rRNA    FALSE                <NA>
3     6M1-18    FALSE                <NA>
4      7M1-2    FALSE                <NA>
5        7SK    FALSE               RN7SK
6      1-Dec    FALSE  BHLHE40 /// DELEC1
7      1-Mar    FALSE  MTARC1 /// MARCHF1
8      2-Mar    FALSE  MTARC2 /// MARCHF2
9      1-Mar    FALSE  MTARC1 /// MARCHF1
10    10-Mar    FALSE            MARCHF10
11    11-Mar    FALSE            MARCHF11
12     2-Mar    FALSE  MTARC2 /// MARCHF2
13     3-Mar    FALSE             MARCHF3
14     4-Mar    FALSE             MARCHF4
15     5-Mar    FALSE             MARCHF5
16     6-Mar    FALSE             MARCHF6
17     7-Mar    FALSE             MARCHF7
18     8-Mar    FALSE             MARCHF8
19     9-Mar    FALSE             MARCHF9
20    15-Sep    FALSE             SELENOF
21     1-Sep    FALSE             SEPTIN1
22    10-Sep    FALSE            SEPTIN10
23    11-Sep    FALSE            SEPTIN11
24    12-Sep    FALSE            SEPTIN12
25    14-Sep    FALSE            SEPTIN14
26     2-Sep    FALSE SEPTIN2 /// SEPTIN6
27     3-Sep    FALSE             SEPTIN3
28     4-Sep    FALSE             SEPTIN4
29     6-Sep    FALSE             SEPTIN6
30     7-Sep    FALSE             SEPTIN7
31     8-Sep    FALSE             SEPTIN8
32     9-Sep    FALSE             SEPTIN9

All NIH-funded data must be made freely accessible

Data Sharing and Public Access Policies

Public online data

Systematic Review of Supervised Machine Learning Models in Prediction of Medical Conditions 2022

complete.cases()

Count the number of rows in a data frame that have missing values with 

sum(!complete.cases(dF))
> tmp <- matrix(1:6, 3, 2)
> tmp
     [,1] [,2]
[1,]    1    4
[2,]    2    5
[3,]    3    6
> tmp[2,1] <- NA
> complete.cases(tmp)
[1]  TRUE FALSE  TRUE

Wrangling categorical data in R

https://peerj.com/preprints/3163.pdf

Some approaches:

  • options(stringAsFactors=FALSE)
  • Use the tidyverse package

Base R approach: 

GSS <- read.csv("XXX.csv")
GSS$BaseLaborStatus <- GSS$LaborStatus
levels(GSS$BaseLaborStatus)
summary(GSS$BaseLaborStatus)
GSS$BaseLaborStatus <- as.character(GSS$BaseLaborStatus)
GSS$BaseLaborStatus[GSS$BaseLaborStatus == "Temp not working"] <- "Temporarily not working"
GSS$BaseLaborStatus[GSS$BaseLaborStatus == "Unempl, laid off"] <- "Unemployed, laid off"
GSS$BaseLaborStatus[GSS$BaseLaborStatus == "Working fulltime"] <- "Working full time"
GSS$BaseLaborStatus[GSS$BaseLaborStatus == "Working parttime"] <- "Working part time"
GSS$BaseLaborStatus <- factor(GSS$BaseLaborStatus)

Tidyverse approach: 

GSS <- GSS %>%
    mutate(tidyLaborStatus =
        recode(LaborStatus,
            `Temp not working` = "Temporarily not working",
            `Unempl, laid off` = "Unemployed, laid off",
            `Working fulltime` = "Working full time",
            `Working parttime ` = "Working part time"))

NIH CBIIT

http://datascience.cancer.gov/

Seminars

NCI Data science webinar series

Reproducibility

Bioinformatics advice I wish I learned 10 years ago from NIH

Project and Data Organization

Project Organization
proj
├── dev
│   ├── clustering.Rmd
│   └── dim_reduce.Rmd
├── doc
├── output
│   ├── 2019-05-10
│   ├── 2019-05-19
│   └── 2019-05-21
├── README.Rmd
├── renv
├── rmd
└── scripts
Data Organization
data
├── annotations
│   ├── clue_drug_repurposing_hub
│   │   ├── repurposing_drugs_20180907.txt
│   │   └── repurposing_samples_20180907.txt
│   └── ...
├── containers
│   └── singularity
│       └── sclc-george2015
├── projects
│   ├── nih
│   │   ├── mm-feature-selection
│   │   ├── mm-p3-variants
│   │   └── sclc-doe
├── public
│   └── human
│       ├── array_express
│       ├── geo
│       │   └── GSE6477
│       │       ├── processed
│       │       │   ├── GSE6477_expr.csv
│       │       │   └── sample_metadata.csv
│       │       └── raw
│       │           ├── GPL96.soft
│       │           └── GSE6477_series_matrix.txt.gz
└── ref
    └── human
        ├── agilent
        ├── gatk
        ├── gencode-v30
        └── rRNA

Container

Data Science for Startups: Containers Building reproducible setups for machine learning

Big data

Hadoop

Spark

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