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student56yash / Assessment-3-part-1

SLE712 Bioinformatics assessment details
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Part A question number 4 #2

Open Dhanusha782 opened 4 years ago

Dhanusha782 commented 4 years ago

Below I have pasted R studio codes till question number 4, and there is an issue on question number 4.

Read the file

download.file("https://raw.githubusercontent.com/markziemann/SLE712_files/master/bioinfo_asst3_part1_files/gene_expression.tsv",destfile="gene_expression.tsv") x<-read.table("gene_expression.tsv") typeof(x) head(x) str(x)

x <- read.table("gene_expression.tsv", header = TRUE , stringsAsFactors = FALSE , row.names = 1, sep="\t") head(x) str(x)

Create new column for mean values

x$Mean<- rowMeans(x) head(x)

10 genes with the higher mean values

head(ord<-x[order(-x$Mean),],n=10)

Number of the gene with the mean value above 10

student56yash commented 4 years ago

To calculate the number of genes, I used which(B<-rowMeans(x)<10)

it gives total genes 43,697 (42124+1573) is it correct?

Dhanusha782 commented 4 years ago

this was the answer I got from cording "omitted 42124 entries"

student56yash commented 4 years ago

It indicates 1537 genes and omitted 42124. I think the combination of these 2 gives number of genes with mean<10