4Cker with 1 condition, no replicates

[tlgolan]

Hi, I am trying to create '4Cker' object by using this code: my_obj = createR4CkerObjectFromDFs(dfs =counts_W_PE, bait_chr="chr5", bait_coord= start_primer, bait_name = "Nppb", primary_enz = "AGATCT", samples ="PE_Nppb_1", conditions = "PE", replicates = 1, species = "rn", output_dir = getwd()) While counts_W_PE is a data frame object (created in R), start_primer- the start position of the primer, the species is Rattus Norvegicus. Unfortunately, I don't have biological replicates in this 4Cseq experiment. For some reason I get this error:

Error in createR4CkerObjectFromDFs(dfs = counts_W_PE, bait_chr = "chr5", : Number of samples does not match

I will be glad for some insights. Thanks, Tal

[rr1859]

Do you only have 1 column in counts_W_PE?

Ramya

On Jul 21, 2016, at 3:34 PM, tlgolan notifications@github.com wrote:

Hi, I am trying to create '4Cker' object by using this code: my_obj = createR4CkerObjectFromDFs(dfs =counts_W_PE, bait_chr="chr5", bait_coord= start_primer, bait_name = "Nppb", primary_enz = "AGATCT", samples ="PE_Nppb_1", conditions = "PE", replicates = 1, species = "rn", output_dir = getwd()) While counts_W_PE is a data frame object (created in R), start_primer- the start position of the primer, the species is Rattus Norvegicus. Unfortunately, I don't have biological replicates in this 4Cseq experiment. For some reason I get this error:

Error in createR4CkerObjectFromDFs(dfs = counts_W_PE, bait_chr = "chr5", : Number of samples does not match

I will be glad for some insights. Thanks, Tal

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rr1859]

counts_W_PE should be a 4 column data.frame with chr, start,end, count for each fragment - is that what you have?

[tlgolan]

This is exactly what I have

On Thursday, July 21, 2016 10:40 PM, Ramya Raviram <notifications@github.com> wrote:

counts_W_PE should be a 4 column data.frame with chr, start,end, count for each fragment - is that what you have?— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[tlgolan]

No, I have four columns: chr name, start position of the fragment, end position of the fragment and counts

On Thursday, July 21, 2016 10:36 PM, Ramya Raviram <notifications@github.com> wrote:

Do you only have 1 column in counts_W_PE?

Ramya

On Jul 21, 2016, at 3:34 PM, tlgolan notifications@github.com wrote:

Hi, I am trying to create '4Cker' object by using this code: my_obj = createR4CkerObjectFromDFs(dfs =counts_W_PE, bait_chr="chr5", bait_coord= start_primer, bait_name = "Nppb", primary_enz = "AGATCT", samples ="PE_Nppb_1", conditions = "PE", replicates = 1, species = "rn", output_dir = getwd()) While counts_W_PE is a data frame object (created in R), start_primer- the start position of the primer, the species is Rattus Norvegicus. Unfortunately, I don't have biological replicates in this 4Cseq experiment. For some reason I get this error:

Error in createR4CkerObjectFromDFs(dfs = counts_W_PE, bait_chr = "chr5", : Number of samples does not match

I will be glad for some insights. Thanks, Tal

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[tlgolan]

For example:> head(counts_W_PE)    V1    V2    V3 Weizmann_PE 1 chr5    43  3301           0 2 chr5  3308  3776           0 3 chr5  3783  6299           0 4 chr5  6306  8431           0 5 chr5  8438 11767           0 6 chr5 11774 12246           0

On Thursday, July 21, 2016 10:40 PM, Ramya Raviram <notifications@github.com> wrote:

counts_W_PE should be a 4 column data.frame with chr, start,end, count for each fragment - is that what you have?— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rr1859]

So for the function, dfs is just variable names for the different data frames so I would change it to my_obj = createR4CkerObjectFromDFs(dfs =c("counts_W_PE"), bait_chr="chr5",...

[tlgolan]

Great! It works! Thanks